Starting phenix.real_space_refine on Sat Jun 21 18:40:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmv_44712/06_2025/9bmv_44712.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15646 2.51 5 N 4254 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3043, 24503 Classifications: {'peptide': 3043} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2909} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.89, per 1000 atoms: 0.56 Number of scatterers: 24616 At special positions: 0 Unit cell: (153.649, 156.742, 133.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 9 15.00 Mg 1 11.99 O 4584 8.00 N 4254 7.00 C 15646 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: 6.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 63.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1349 through 1354 removed outlier: 5.937A pdb=" N VAL A1352 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1354 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 4.140A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1471 Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1508 through 1509 No H-bonds generated for 'chain 'A' and resid 1508 through 1509' Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.811A pdb=" N ALA A1520 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.179A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.630A pdb=" N THR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A1566 " --> pdb=" O PRO A1562 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1647 through 1652 removed outlier: 4.199A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.634A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1772 removed outlier: 3.583A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.659A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.679A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1912 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 3.733A pdb=" N MET A1941 " --> pdb=" O ASP A1937 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.619A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 removed outlier: 3.500A pdb=" N ARG A2118 " --> pdb=" O GLU A2114 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.246A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2245 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 4.118A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2314 through 2320 removed outlier: 4.339A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.542A pdb=" N VAL A2356 " --> pdb=" O THR A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 3.910A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.934A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.834A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.566A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.555A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.642A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 3.892A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.927A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2834 through 2837 Processing helix chain 'A' and resid 2840 through 2858 removed outlier: 3.739A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.515A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 removed outlier: 3.540A pdb=" N LEU A2946 " --> pdb=" O GLY A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2968 through 2984 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.975A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.931A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.902A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 removed outlier: 3.571A pdb=" N ARG A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.680A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3704 through 3721 removed outlier: 3.584A pdb=" N GLN A3709 " --> pdb=" O ARG A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 3.807A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 removed outlier: 3.663A pdb=" N LEU A3761 " --> pdb=" O GLY A3758 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.339A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.715A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3911 through 3913 No H-bonds generated for 'chain 'A' and resid 3911 through 3913' Processing helix chain 'A' and resid 3928 through 3940 removed outlier: 3.572A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3963 removed outlier: 3.781A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4014 through 4017 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.538A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.633A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.775A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.543A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.501A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 4.037A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.544A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4348 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.328A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.085A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.608A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1665 removed outlier: 10.593A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.113A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 6.840A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2325 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2710 through 2712 removed outlier: 6.209A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 5.849A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 3.589A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.584A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.104A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3655 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.148A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 7.057A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.090A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4582 through 4584 removed outlier: 3.718A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4569 through 4570 1424 hydrogen bonds defined for protein. 4152 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: 17.25 Time building geometry restraints manager: 7.90 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: 8115 1.34 - 1.46: 4808 1.46 - 1.58: 12000 1.58 - 1.69: 13 1.69 - 1.81: 206 Bond restraints: 25142 Sorted by residual: bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N ASP A1606 " pdb=" CA ASP A1606 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.87e+00 bond pdb=" N LEU A1608 " pdb=" CA LEU A1608 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.61e+00 bond pdb=" N PHE A1568 " pdb=" CA PHE A1568 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.48e+00 bond pdb=" N LEU A1607 " pdb=" CA LEU A1607 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.26e+00 ... (remaining 25137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 33214 1.69 - 3.37: 740 3.37 - 5.06: 103 5.06 - 6.75: 27 6.75 - 8.44: 5 Bond angle restraints: 34089 Sorted by residual: angle pdb=" C GLN A4062 " pdb=" N ASN A4063 " pdb=" CA ASN A4063 " ideal model delta sigma weight residual 122.46 128.18 -5.72 1.41e+00 5.03e-01 1.65e+01 angle pdb=" CA THR A1565 " pdb=" CB THR A1565 " pdb=" OG1 THR A1565 " ideal model delta sigma weight residual 109.60 105.00 4.60 1.50e+00 4.44e-01 9.40e+00 angle pdb=" N GLU A4414 " pdb=" CA GLU A4414 " pdb=" CB GLU A4414 " ideal model delta sigma weight residual 110.16 114.57 -4.41 1.48e+00 4.57e-01 8.89e+00 angle pdb=" CB MET A4157 " pdb=" CG MET A4157 " pdb=" SD MET A4157 " ideal model delta sigma weight residual 112.70 121.14 -8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" CA MET A2686 " pdb=" CB MET A2686 " pdb=" CG MET A2686 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 ... (remaining 34084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13657 17.96 - 35.92: 1309 35.92 - 53.88: 208 53.88 - 71.84: 61 71.84 - 89.80: 23 Dihedral angle restraints: 15258 sinusoidal: 6348 harmonic: 8910 Sorted by residual: dihedral pdb=" CD ARG A1567 " pdb=" NE ARG A1567 " pdb=" CZ ARG A1567 " pdb=" NH1 ARG A1567 " ideal model delta sinusoidal sigma weight residual 0.00 69.17 -69.17 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CG ARG A1567 " pdb=" CD ARG A1567 " pdb=" NE ARG A1567 " pdb=" CZ ARG A1567 " ideal model delta sinusoidal sigma weight residual 90.00 3.50 86.50 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -127.60 67.60 1 2.00e+01 2.50e-03 1.49e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2716 0.038 - 0.075: 800 0.075 - 0.113: 267 0.113 - 0.151: 32 0.151 - 0.189: 6 Chirality restraints: 3821 Sorted by residual: chirality pdb=" CB ILE A3662 " pdb=" CA ILE A3662 " pdb=" CG1 ILE A3662 " pdb=" CG2 ILE A3662 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CG LEU A2075 " pdb=" CB LEU A2075 " pdb=" CD1 LEU A2075 " pdb=" CD2 LEU A2075 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" C1' ADP A4703 " pdb=" C2' ADP A4703 " pdb=" N9 ADP A4703 " pdb=" O4' ADP A4703 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 3818 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1567 " 1.003 9.50e-02 1.11e+02 4.49e-01 1.23e+02 pdb=" NE ARG A1567 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A1567 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A1567 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1567 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4414 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" CD GLU A4414 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A4414 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A4414 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A4410 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C PHE A4410 " -0.043 2.00e-02 2.50e+03 pdb=" O PHE A4410 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A4411 " 0.014 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 164 2.51 - 3.11: 18981 3.11 - 3.71: 40240 3.71 - 4.30: 53252 4.30 - 4.90: 88197 Nonbonded interactions: 200834 Sorted by model distance: nonbonded pdb=" O3B ATP A4702 " pdb="MG MG A4705 " model vdw 1.916 2.170 nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4705 " model vdw 1.954 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4705 " model vdw 2.082 2.170 nonbonded pdb=" O GLY A1911 " pdb=" OG SER A1915 " model vdw 2.147 3.040 nonbonded pdb=" O SER A4480 " pdb=" OG SER A4483 " model vdw 2.160 3.040 ... (remaining 200829 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=1.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 68.020 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25142 Z= 0.161 Angle : 0.619 8.436 34089 Z= 0.331 Chirality : 0.040 0.189 3821 Planarity : 0.008 0.449 4367 Dihedral : 14.580 89.800 9470 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 3035 helix: 1.91 (0.12), residues: 1732 sheet: -0.71 (0.34), residues: 260 loop : 0.35 (0.21), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A2584 HIS 0.011 0.001 HIS A2689 PHE 0.027 0.002 PHE A2992 TYR 0.017 0.001 TYR A3026 ARG 0.007 0.000 ARG A1567 Details of bonding type rmsd hydrogen bonds : bond 0.13102 ( 1424) hydrogen bonds : angle 5.15873 ( 4152) covalent geometry : bond 0.00330 (25142) covalent geometry : angle 0.61906 (34089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1575 PHE cc_start: 0.6945 (t80) cc_final: 0.6693 (t80) REVERT: A 2047 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 2053 MET cc_start: 0.8049 (mmt) cc_final: 0.7660 (mmt) REVERT: A 2376 ASN cc_start: 0.8973 (m-40) cc_final: 0.8720 (m-40) REVERT: A 2535 ILE cc_start: 0.8942 (tt) cc_final: 0.8516 (mt) REVERT: A 2798 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7962 (tm-30) REVERT: A 2839 GLU cc_start: 0.8047 (mp0) cc_final: 0.7684 (mp0) REVERT: A 3026 TYR cc_start: 0.8510 (t80) cc_final: 0.8306 (t80) REVERT: A 3030 MET cc_start: 0.8772 (mmp) cc_final: 0.8407 (mmt) REVERT: A 3792 GLN cc_start: 0.8483 (tp40) cc_final: 0.8277 (tp40) REVERT: A 3913 GLU cc_start: 0.8746 (mp0) cc_final: 0.8545 (mp0) REVERT: A 4095 MET cc_start: 0.8183 (tmm) cc_final: 0.7922 (tmm) outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.4035 time to fit residues: 266.7004 Evaluate side-chains 302 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 238 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1699 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2439 HIS A2752 ASN A2964 HIS A3175 HIS A3535 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4404 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088630 restraints weight = 69082.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090753 restraints weight = 39237.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092112 restraints weight = 27724.234| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25142 Z= 0.130 Angle : 0.594 9.796 34089 Z= 0.298 Chirality : 0.040 0.212 3821 Planarity : 0.004 0.047 4367 Dihedral : 6.133 84.831 3377 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 7.80 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 3035 helix: 1.96 (0.12), residues: 1766 sheet: -0.86 (0.34), residues: 257 loop : 0.35 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1701 HIS 0.009 0.001 HIS A4389 PHE 0.019 0.002 PHE A4161 TYR 0.022 0.001 TYR A2748 ARG 0.006 0.000 ARG A4400 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1424) hydrogen bonds : angle 4.29432 ( 4152) covalent geometry : bond 0.00286 (25142) covalent geometry : angle 0.59450 (34089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: 0.6297 (mmm) cc_final: 0.5694 (ptt) REVERT: A 1669 ASP cc_start: 0.8342 (t0) cc_final: 0.8089 (t0) REVERT: A 1769 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7354 (mmm) REVERT: A 2047 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 2262 ASP cc_start: 0.8401 (p0) cc_final: 0.7725 (p0) REVERT: A 2333 LEU cc_start: 0.6299 (mt) cc_final: 0.6069 (mp) REVERT: A 2361 MET cc_start: 0.8011 (tpp) cc_final: 0.7697 (tpt) REVERT: A 2372 ASP cc_start: 0.8007 (p0) cc_final: 0.7372 (m-30) REVERT: A 2376 ASN cc_start: 0.8955 (m-40) cc_final: 0.8658 (m-40) REVERT: A 2471 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 2535 ILE cc_start: 0.8974 (tt) cc_final: 0.8583 (mt) REVERT: A 2798 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7991 (tm-30) REVERT: A 2855 LEU cc_start: 0.8866 (tt) cc_final: 0.8519 (pp) REVERT: A 2962 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7741 (mmtm) REVERT: A 4347 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8319 (tm-30) outliers start: 37 outliers final: 23 residues processed: 358 average time/residue: 0.3607 time to fit residues: 209.2747 Evaluate side-chains 311 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2692 PHE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3143 ILE Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4603 SER Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 8 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 111 optimal weight: 0.0070 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083077 restraints weight = 74336.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085331 restraints weight = 39894.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.086753 restraints weight = 27030.191| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25142 Z= 0.181 Angle : 0.606 12.793 34089 Z= 0.304 Chirality : 0.041 0.208 3821 Planarity : 0.004 0.048 4367 Dihedral : 6.109 88.694 3377 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 10.27 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3035 helix: 1.91 (0.12), residues: 1768 sheet: -1.20 (0.33), residues: 262 loop : 0.35 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1701 HIS 0.010 0.001 HIS A1559 PHE 0.026 0.002 PHE A2635 TYR 0.019 0.002 TYR A1618 ARG 0.005 0.000 ARG A3743 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1424) hydrogen bonds : angle 4.23865 ( 4152) covalent geometry : bond 0.00413 (25142) covalent geometry : angle 0.60565 (34089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: 0.6346 (mmm) cc_final: 0.5859 (ptt) REVERT: A 1507 MET cc_start: 0.5583 (mmm) cc_final: 0.5292 (mmm) REVERT: A 1531 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7654 (mmt) REVERT: A 1575 PHE cc_start: 0.7235 (t80) cc_final: 0.6887 (t80) REVERT: A 1589 MET cc_start: 0.6128 (mmm) cc_final: 0.5097 (mtp) REVERT: A 1669 ASP cc_start: 0.8518 (t0) cc_final: 0.8229 (t70) REVERT: A 1769 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: A 1960 PHE cc_start: 0.8163 (t80) cc_final: 0.7828 (t80) REVERT: A 2262 ASP cc_start: 0.8294 (p0) cc_final: 0.7980 (p0) REVERT: A 2372 ASP cc_start: 0.8288 (p0) cc_final: 0.7623 (m-30) REVERT: A 2376 ASN cc_start: 0.9009 (m-40) cc_final: 0.8772 (m-40) REVERT: A 2471 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 2535 ILE cc_start: 0.9087 (tt) cc_final: 0.8750 (mt) REVERT: A 2798 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7977 (tm-30) REVERT: A 2837 LEU cc_start: 0.8668 (mp) cc_final: 0.8098 (mp) REVERT: A 2855 LEU cc_start: 0.8942 (tt) cc_final: 0.8591 (pp) REVERT: A 3005 LEU cc_start: 0.8688 (mt) cc_final: 0.8421 (mt) REVERT: A 3633 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 4347 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 53 outliers final: 35 residues processed: 341 average time/residue: 0.3560 time to fit residues: 198.7201 Evaluate side-chains 315 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2958 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4504 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 271 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN A4012 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.109599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083506 restraints weight = 73970.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085746 restraints weight = 39184.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087179 restraints weight = 26405.315| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25142 Z= 0.148 Angle : 0.582 11.623 34089 Z= 0.291 Chirality : 0.041 0.178 3821 Planarity : 0.004 0.048 4367 Dihedral : 6.027 85.025 3377 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.96 % Allowed : 12.16 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3035 helix: 1.90 (0.12), residues: 1773 sheet: -1.23 (0.33), residues: 257 loop : 0.36 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1701 HIS 0.009 0.001 HIS A1559 PHE 0.021 0.001 PHE A2708 TYR 0.017 0.001 TYR A1618 ARG 0.006 0.000 ARG A2273 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1424) hydrogen bonds : angle 4.09728 ( 4152) covalent geometry : bond 0.00335 (25142) covalent geometry : angle 0.58162 (34089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: 0.6389 (mmm) cc_final: 0.6122 (ptt) REVERT: A 1507 MET cc_start: 0.5920 (mmm) cc_final: 0.5642 (mmm) REVERT: A 1531 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7596 (mmt) REVERT: A 1589 MET cc_start: 0.6142 (mmm) cc_final: 0.5110 (mtp) REVERT: A 1960 PHE cc_start: 0.8142 (t80) cc_final: 0.7854 (t80) REVERT: A 2012 MET cc_start: 0.7852 (tpp) cc_final: 0.7413 (tpp) REVERT: A 2273 ARG cc_start: 0.7877 (mmp80) cc_final: 0.7656 (mmp80) REVERT: A 2372 ASP cc_start: 0.8342 (p0) cc_final: 0.8113 (p0) REVERT: A 2376 ASN cc_start: 0.9051 (m-40) cc_final: 0.8771 (m-40) REVERT: A 2471 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 2510 MET cc_start: 0.7613 (ttm) cc_final: 0.7226 (ttm) REVERT: A 2535 ILE cc_start: 0.9164 (tt) cc_final: 0.8795 (mt) REVERT: A 2789 GLN cc_start: 0.8373 (mp10) cc_final: 0.7965 (mp10) REVERT: A 2837 LEU cc_start: 0.8684 (mp) cc_final: 0.8155 (mp) REVERT: A 2851 ASP cc_start: 0.8047 (p0) cc_final: 0.7769 (p0) REVERT: A 2855 LEU cc_start: 0.8917 (tt) cc_final: 0.8581 (pp) REVERT: A 2962 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7867 (mmtm) REVERT: A 3005 LEU cc_start: 0.8728 (mt) cc_final: 0.8434 (mt) REVERT: A 3927 LEU cc_start: 0.8294 (tp) cc_final: 0.7787 (tp) REVERT: A 4078 ASN cc_start: 0.8538 (m110) cc_final: 0.8316 (m-40) REVERT: A 4346 MET cc_start: 0.9106 (mmt) cc_final: 0.8798 (mmt) REVERT: A 4347 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8489 (tm-30) outliers start: 53 outliers final: 34 residues processed: 335 average time/residue: 0.3777 time to fit residues: 204.6280 Evaluate side-chains 302 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2958 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4504 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 14 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 287 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 260 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 285 optimal weight: 0.0970 chunk 223 optimal weight: 5.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3057 GLN A3092 ASN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN A4012 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.118323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092172 restraints weight = 73562.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094500 restraints weight = 38574.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096018 restraints weight = 25454.996| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25142 Z= 0.109 Angle : 0.571 10.194 34089 Z= 0.280 Chirality : 0.039 0.176 3821 Planarity : 0.004 0.047 4367 Dihedral : 5.777 78.532 3377 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 13.78 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 3035 helix: 1.99 (0.12), residues: 1774 sheet: -1.24 (0.32), residues: 266 loop : 0.39 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1701 HIS 0.009 0.001 HIS A1559 PHE 0.032 0.001 PHE A2635 TYR 0.019 0.001 TYR A3026 ARG 0.008 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1424) hydrogen bonds : angle 4.00582 ( 4152) covalent geometry : bond 0.00235 (25142) covalent geometry : angle 0.57122 (34089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7432 (p) REVERT: A 1531 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: A 1575 PHE cc_start: 0.7210 (t80) cc_final: 0.6946 (t80) REVERT: A 1589 MET cc_start: 0.6012 (mmm) cc_final: 0.4965 (mtp) REVERT: A 1960 PHE cc_start: 0.8002 (t80) cc_final: 0.7757 (t80) REVERT: A 2012 MET cc_start: 0.7804 (tpp) cc_final: 0.7266 (tpp) REVERT: A 2145 MET cc_start: 0.8493 (tpp) cc_final: 0.8251 (mmt) REVERT: A 2372 ASP cc_start: 0.8240 (p0) cc_final: 0.8000 (p0) REVERT: A 2376 ASN cc_start: 0.9029 (m-40) cc_final: 0.8744 (m-40) REVERT: A 2471 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 2535 ILE cc_start: 0.9119 (tt) cc_final: 0.8807 (mt) REVERT: A 2584 TRP cc_start: 0.8297 (m-10) cc_final: 0.7933 (m-10) REVERT: A 2594 CYS cc_start: 0.7189 (t) cc_final: 0.6449 (t) REVERT: A 2712 CYS cc_start: 0.7285 (t) cc_final: 0.6598 (t) REVERT: A 2789 GLN cc_start: 0.8255 (mp10) cc_final: 0.7932 (mp10) REVERT: A 2837 LEU cc_start: 0.8598 (mp) cc_final: 0.8069 (mp) REVERT: A 2851 ASP cc_start: 0.7979 (p0) cc_final: 0.7681 (p0) REVERT: A 2855 LEU cc_start: 0.8866 (tt) cc_final: 0.8568 (pp) REVERT: A 2962 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7878 (mmtm) REVERT: A 3927 LEU cc_start: 0.8089 (tp) cc_final: 0.7572 (tp) REVERT: A 4018 MET cc_start: 0.7381 (mtm) cc_final: 0.7064 (mtm) REVERT: A 4078 ASN cc_start: 0.8415 (m110) cc_final: 0.8198 (m-40) REVERT: A 4343 MET cc_start: 0.9330 (ttm) cc_final: 0.8775 (ttm) REVERT: A 4346 MET cc_start: 0.9096 (mmt) cc_final: 0.8810 (mmt) REVERT: A 4347 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8457 (tm-30) outliers start: 49 outliers final: 35 residues processed: 332 average time/residue: 0.3689 time to fit residues: 202.1323 Evaluate side-chains 306 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4504 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 234 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 120 optimal weight: 0.0170 chunk 79 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN A4012 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.112704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086025 restraints weight = 76234.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088509 restraints weight = 39047.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090094 restraints weight = 25825.121| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25142 Z= 0.135 Angle : 0.576 10.689 34089 Z= 0.284 Chirality : 0.040 0.179 3821 Planarity : 0.004 0.046 4367 Dihedral : 5.577 70.149 3377 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.03 % Allowed : 14.41 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 3035 helix: 2.01 (0.13), residues: 1763 sheet: -1.19 (0.32), residues: 266 loop : 0.37 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1701 HIS 0.008 0.001 HIS A1559 PHE 0.041 0.001 PHE A4410 TYR 0.018 0.001 TYR A2582 ARG 0.004 0.000 ARG A2977 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 1424) hydrogen bonds : angle 4.01314 ( 4152) covalent geometry : bond 0.00306 (25142) covalent geometry : angle 0.57623 (34089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7421 (p) REVERT: A 1531 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7596 (mmt) REVERT: A 1579 MET cc_start: 0.8468 (mmm) cc_final: 0.8258 (mmm) REVERT: A 1589 MET cc_start: 0.6103 (mmm) cc_final: 0.5076 (mtp) REVERT: A 1960 PHE cc_start: 0.8037 (t80) cc_final: 0.7787 (t80) REVERT: A 2012 MET cc_start: 0.7893 (tpp) cc_final: 0.7508 (tpp) REVERT: A 2145 MET cc_start: 0.8503 (tpp) cc_final: 0.8227 (mmt) REVERT: A 2372 ASP cc_start: 0.8309 (p0) cc_final: 0.8005 (p0) REVERT: A 2376 ASN cc_start: 0.8984 (m-40) cc_final: 0.8685 (m-40) REVERT: A 2455 LEU cc_start: 0.8785 (mp) cc_final: 0.8557 (mp) REVERT: A 2471 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 2510 MET cc_start: 0.7523 (ttm) cc_final: 0.7130 (ttm) REVERT: A 2535 ILE cc_start: 0.9155 (tt) cc_final: 0.8842 (mt) REVERT: A 2671 MET cc_start: 0.8058 (tpp) cc_final: 0.7803 (tpt) REVERT: A 2789 GLN cc_start: 0.8249 (mp10) cc_final: 0.7946 (mp10) REVERT: A 2837 LEU cc_start: 0.8676 (mp) cc_final: 0.8168 (mp) REVERT: A 2855 LEU cc_start: 0.8876 (tt) cc_final: 0.8602 (pp) REVERT: A 2869 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7456 (mmm160) REVERT: A 3005 LEU cc_start: 0.8670 (mt) cc_final: 0.8417 (mt) REVERT: A 3601 MET cc_start: 0.8856 (mmm) cc_final: 0.8593 (mmt) REVERT: A 4078 ASN cc_start: 0.8492 (m110) cc_final: 0.8263 (m-40) REVERT: A 4346 MET cc_start: 0.9049 (mmt) cc_final: 0.8789 (mmt) REVERT: A 4347 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8422 (tm-30) outliers start: 55 outliers final: 40 residues processed: 318 average time/residue: 0.3632 time to fit residues: 189.9886 Evaluate side-chains 312 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2958 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4504 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 35 optimal weight: 0.3980 chunk 282 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 273 optimal weight: 0.0270 chunk 18 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.4640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.114285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087838 restraints weight = 76271.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090344 restraints weight = 38724.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091937 restraints weight = 25477.779| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25142 Z= 0.108 Angle : 0.582 10.071 34089 Z= 0.282 Chirality : 0.039 0.182 3821 Planarity : 0.004 0.046 4367 Dihedral : 5.344 60.016 3377 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.55 % Allowed : 15.48 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.16), residues: 3035 helix: 2.07 (0.13), residues: 1755 sheet: -1.16 (0.33), residues: 258 loop : 0.32 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1701 HIS 0.007 0.001 HIS A1559 PHE 0.051 0.001 PHE A4410 TYR 0.024 0.001 TYR A3026 ARG 0.006 0.000 ARG A2273 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1424) hydrogen bonds : angle 3.93281 ( 4152) covalent geometry : bond 0.00233 (25142) covalent geometry : angle 0.58232 (34089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7430 (p) REVERT: A 1507 MET cc_start: 0.5094 (mmm) cc_final: 0.4617 (mmm) REVERT: A 1531 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7555 (mmt) REVERT: A 1589 MET cc_start: 0.6166 (mmm) cc_final: 0.5174 (mtp) REVERT: A 1960 PHE cc_start: 0.7924 (t80) cc_final: 0.7676 (t80) REVERT: A 2012 MET cc_start: 0.7767 (tpp) cc_final: 0.7512 (tpp) REVERT: A 2145 MET cc_start: 0.8428 (tpp) cc_final: 0.8127 (mmt) REVERT: A 2372 ASP cc_start: 0.8188 (p0) cc_final: 0.7870 (p0) REVERT: A 2376 ASN cc_start: 0.8944 (m-40) cc_final: 0.8667 (m-40) REVERT: A 2455 LEU cc_start: 0.8750 (mp) cc_final: 0.8313 (mp) REVERT: A 2471 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 2535 ILE cc_start: 0.9156 (tt) cc_final: 0.8847 (mt) REVERT: A 2584 TRP cc_start: 0.8231 (m-10) cc_final: 0.7939 (m-10) REVERT: A 2712 CYS cc_start: 0.6996 (t) cc_final: 0.6087 (t) REVERT: A 2789 GLN cc_start: 0.8306 (mp10) cc_final: 0.7997 (mp10) REVERT: A 2837 LEU cc_start: 0.8669 (mp) cc_final: 0.8153 (mp) REVERT: A 2851 ASP cc_start: 0.8013 (p0) cc_final: 0.7731 (p0) REVERT: A 2855 LEU cc_start: 0.8848 (tt) cc_final: 0.8581 (pp) REVERT: A 3086 PHE cc_start: 0.7633 (m-80) cc_final: 0.7428 (m-80) REVERT: A 3601 MET cc_start: 0.8856 (mmm) cc_final: 0.8586 (mmt) REVERT: A 3927 LEU cc_start: 0.8244 (tp) cc_final: 0.7723 (tp) REVERT: A 4078 ASN cc_start: 0.8471 (m110) cc_final: 0.8242 (m-40) REVERT: A 4192 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7810 (mm-30) REVERT: A 4347 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 4377 MET cc_start: 0.8299 (mmm) cc_final: 0.5999 (mpp) outliers start: 42 outliers final: 34 residues processed: 318 average time/residue: 0.3619 time to fit residues: 189.9391 Evaluate side-chains 307 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4444 GLN Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 248 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 145 optimal weight: 0.0570 chunk 169 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN A2346 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080683 restraints weight = 74067.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082743 restraints weight = 40791.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084096 restraints weight = 28314.483| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25142 Z= 0.227 Angle : 0.663 10.473 34089 Z= 0.328 Chirality : 0.042 0.187 3821 Planarity : 0.004 0.063 4367 Dihedral : 5.508 65.482 3377 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 15.85 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.16), residues: 3035 helix: 1.86 (0.12), residues: 1769 sheet: -1.15 (0.32), residues: 269 loop : 0.32 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1701 HIS 0.008 0.001 HIS A3175 PHE 0.035 0.002 PHE A4410 TYR 0.016 0.002 TYR A2496 ARG 0.004 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1424) hydrogen bonds : angle 4.13901 ( 4152) covalent geometry : bond 0.00511 (25142) covalent geometry : angle 0.66310 (34089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7685 (p) REVERT: A 1507 MET cc_start: 0.5027 (mmm) cc_final: 0.4600 (mmm) REVERT: A 1589 MET cc_start: 0.6118 (mmm) cc_final: 0.5117 (mtp) REVERT: A 1958 ASP cc_start: 0.8162 (t0) cc_final: 0.7920 (t0) REVERT: A 1960 PHE cc_start: 0.8197 (t80) cc_final: 0.7925 (t80) REVERT: A 2012 MET cc_start: 0.8141 (tpp) cc_final: 0.7903 (tpp) REVERT: A 2145 MET cc_start: 0.8480 (tpp) cc_final: 0.8266 (mmt) REVERT: A 2273 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7368 (mmp80) REVERT: A 2372 ASP cc_start: 0.8455 (p0) cc_final: 0.8058 (p0) REVERT: A 2376 ASN cc_start: 0.8974 (m-40) cc_final: 0.8725 (m-40) REVERT: A 2455 LEU cc_start: 0.8898 (mp) cc_final: 0.8427 (mp) REVERT: A 2471 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 2535 ILE cc_start: 0.9261 (tt) cc_final: 0.8977 (mt) REVERT: A 2670 ASP cc_start: 0.7643 (p0) cc_final: 0.7371 (p0) REVERT: A 2789 GLN cc_start: 0.8265 (mp10) cc_final: 0.7911 (mp10) REVERT: A 2837 LEU cc_start: 0.8757 (mp) cc_final: 0.8298 (mp) REVERT: A 2855 LEU cc_start: 0.8893 (tt) cc_final: 0.8587 (pp) REVERT: A 3005 LEU cc_start: 0.8761 (mt) cc_final: 0.8433 (mt) REVERT: A 3078 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8074 (tpp-160) REVERT: A 4078 ASN cc_start: 0.8529 (m110) cc_final: 0.8297 (m-40) REVERT: A 4347 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 4377 MET cc_start: 0.8244 (mmm) cc_final: 0.5776 (mpp) REVERT: A 4414 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7476 (mt-10) outliers start: 56 outliers final: 37 residues processed: 303 average time/residue: 0.3609 time to fit residues: 179.1737 Evaluate side-chains 285 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2680 ILE Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2958 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4444 GLN Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 LEU Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 85 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2491 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.109268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083268 restraints weight = 73505.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086781 restraints weight = 40974.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087051 restraints weight = 22960.966| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25142 Z= 0.120 Angle : 0.619 9.956 34089 Z= 0.301 Chirality : 0.040 0.182 3821 Planarity : 0.004 0.046 4367 Dihedral : 5.306 57.503 3377 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.59 % Allowed : 16.85 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 3035 helix: 1.99 (0.13), residues: 1766 sheet: -1.20 (0.33), residues: 251 loop : 0.30 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1701 HIS 0.008 0.001 HIS A4187 PHE 0.034 0.001 PHE A4410 TYR 0.018 0.001 TYR A3519 ARG 0.017 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 1424) hydrogen bonds : angle 4.00227 ( 4152) covalent geometry : bond 0.00267 (25142) covalent geometry : angle 0.61905 (34089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 1507 MET cc_start: 0.5284 (mmm) cc_final: 0.4803 (mmm) REVERT: A 1589 MET cc_start: 0.6110 (mmm) cc_final: 0.5132 (mtm) REVERT: A 1960 PHE cc_start: 0.7910 (t80) cc_final: 0.7661 (t80) REVERT: A 2012 MET cc_start: 0.7952 (tpp) cc_final: 0.7568 (tpp) REVERT: A 2145 MET cc_start: 0.8457 (tpp) cc_final: 0.8191 (mmt) REVERT: A 2221 MET cc_start: 0.7893 (mpp) cc_final: 0.7665 (mpp) REVERT: A 2273 ARG cc_start: 0.7642 (mmp80) cc_final: 0.7359 (mmp80) REVERT: A 2333 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6305 (mm) REVERT: A 2372 ASP cc_start: 0.8279 (p0) cc_final: 0.7883 (p0) REVERT: A 2376 ASN cc_start: 0.8979 (m-40) cc_final: 0.8704 (m-40) REVERT: A 2455 LEU cc_start: 0.8828 (mp) cc_final: 0.8333 (mp) REVERT: A 2471 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8450 (tm-30) REVERT: A 2535 ILE cc_start: 0.9206 (tt) cc_final: 0.8947 (mt) REVERT: A 2584 TRP cc_start: 0.8235 (m-10) cc_final: 0.7922 (m-10) REVERT: A 2670 ASP cc_start: 0.7484 (p0) cc_final: 0.7205 (p0) REVERT: A 2789 GLN cc_start: 0.8359 (mp10) cc_final: 0.7996 (mp10) REVERT: A 2837 LEU cc_start: 0.8651 (mp) cc_final: 0.8161 (mp) REVERT: A 2855 LEU cc_start: 0.8847 (tt) cc_final: 0.8576 (pp) REVERT: A 2869 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7180 (mmt180) REVERT: A 3078 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8239 (tpp-160) REVERT: A 4078 ASN cc_start: 0.8644 (m110) cc_final: 0.8406 (m-40) REVERT: A 4347 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 4377 MET cc_start: 0.8276 (mmm) cc_final: 0.5675 (mpp) REVERT: A 4414 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: A 4416 GLU cc_start: 0.8187 (tp30) cc_final: 0.7684 (tp30) outliers start: 43 outliers final: 27 residues processed: 300 average time/residue: 0.3674 time to fit residues: 180.6823 Evaluate side-chains 284 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4444 GLN Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 296 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2299 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.081325 restraints weight = 73250.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083476 restraints weight = 39475.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084868 restraints weight = 26858.465| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25142 Z= 0.166 Angle : 0.647 14.862 34089 Z= 0.316 Chirality : 0.041 0.245 3821 Planarity : 0.004 0.046 4367 Dihedral : 5.313 60.301 3377 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.26 % Allowed : 16.96 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3035 helix: 1.92 (0.12), residues: 1768 sheet: -1.25 (0.33), residues: 251 loop : 0.32 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2275 HIS 0.007 0.001 HIS A4187 PHE 0.042 0.002 PHE A2635 TYR 0.017 0.002 TYR A1618 ARG 0.011 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 1424) hydrogen bonds : angle 4.08997 ( 4152) covalent geometry : bond 0.00379 (25142) covalent geometry : angle 0.64657 (34089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8863 (tt0) REVERT: A 1507 MET cc_start: 0.4973 (mmm) cc_final: 0.4599 (mmm) REVERT: A 1589 MET cc_start: 0.6098 (mmm) cc_final: 0.5134 (mtm) REVERT: A 1960 PHE cc_start: 0.8039 (t80) cc_final: 0.7775 (t80) REVERT: A 2012 MET cc_start: 0.8126 (tpp) cc_final: 0.7816 (tpp) REVERT: A 2145 MET cc_start: 0.8498 (tpp) cc_final: 0.8187 (mmt) REVERT: A 2221 MET cc_start: 0.7892 (mpp) cc_final: 0.7668 (mpp) REVERT: A 2333 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6360 (mm) REVERT: A 2372 ASP cc_start: 0.8391 (p0) cc_final: 0.8049 (p0) REVERT: A 2376 ASN cc_start: 0.9030 (m-40) cc_final: 0.8742 (m-40) REVERT: A 2455 LEU cc_start: 0.8891 (mp) cc_final: 0.8399 (mp) REVERT: A 2471 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8456 (tm-30) REVERT: A 2670 ASP cc_start: 0.7518 (p0) cc_final: 0.7236 (p0) REVERT: A 2789 GLN cc_start: 0.8364 (mp10) cc_final: 0.7991 (mp10) REVERT: A 2837 LEU cc_start: 0.8672 (mp) cc_final: 0.8204 (mp) REVERT: A 2855 LEU cc_start: 0.8874 (tt) cc_final: 0.8586 (pp) REVERT: A 3005 LEU cc_start: 0.8841 (mt) cc_final: 0.8638 (mt) REVERT: A 3078 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8155 (tpp-160) REVERT: A 4078 ASN cc_start: 0.8586 (m110) cc_final: 0.8355 (m-40) REVERT: A 4347 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 4377 MET cc_start: 0.8305 (mmm) cc_final: 0.5768 (mpp) REVERT: A 4414 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: A 4416 GLU cc_start: 0.8266 (tp30) cc_final: 0.7746 (tp30) outliers start: 34 outliers final: 29 residues processed: 285 average time/residue: 0.3649 time to fit residues: 171.6488 Evaluate side-chains 279 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4444 GLN Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 303 optimal weight: 0.5980 chunk 292 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2171 HIS ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3880 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 = 0.3765 r_free = 0.3765 target = 0.107492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081979 restraints weight = 73559.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084496 restraints weight = 41137.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084652 restraints weight = 26134.800| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 25142 Z= 0.199 Angle : 0.758 59.157 34089 Z= 0.403 Chirality : 0.042 0.639 3821 Planarity : 0.004 0.046 4367 Dihedral : 5.334 60.220 3377 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.52 % Allowed : 16.81 % Favored : 81.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3035 helix: 1.92 (0.12), residues: 1768 sheet: -1.26 (0.33), residues: 251 loop : 0.32 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.007 0.001 HIS A4187 PHE 0.024 0.002 PHE A2635 TYR 0.016 0.001 TYR A3519 ARG 0.009 0.000 ARG A3486 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 1424) hydrogen bonds : angle 4.09537 ( 4152) covalent geometry : bond 0.00431 (25142) covalent geometry : angle 0.75828 (34089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8491.29 seconds wall clock time: 147 minutes 47.58 seconds (8867.58 seconds total)