Starting phenix.real_space_refine on Fri Sep 19 10:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmv_44712/09_2025/9bmv_44712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmv_44712/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bmv_44712/09_2025/9bmv_44712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmv_44712/09_2025/9bmv_44712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bmv_44712/09_2025/9bmv_44712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmv_44712/09_2025/9bmv_44712.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.07, per 1000 atoms: 0.21 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: 2.05 Conformation dependent library (CDL) restraints added in 875.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.54 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: 8.27 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.840 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG A1567 TYR 0.017 0.001 TYR A3026 PHE 0.027 0.002 PHE A2992 TRP 0.037 0.002 TRP A2584 HIS 0.011 0.001 HIS A2689 Details of bonding type rmsd covalent geometry : bond 0.00330 (25142) covalent geometry : angle 0.61906 (34089) hydrogen bonds : bond 0.13102 ( 1424) hydrogen bonds : angle 5.15873 ( 4152) *********************** 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 : 0.650 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: 0.1474 time to fit residues: 96.7067 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 : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1699 ASN A2299 GLN A2414 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN 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 = 0.3765 r_free = 0.3765 target = 0.110937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083760 restraints weight = 71812.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085702 restraints weight = 40987.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086981 restraints weight = 29387.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087826 restraints weight = 23996.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088265 restraints weight = 21195.086| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 25142 Z= 0.275 Angle : 0.689 8.804 34089 Z= 0.351 Chirality : 0.043 0.241 3821 Planarity : 0.005 0.048 4367 Dihedral : 6.360 89.647 3377 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.00 % Allowed : 8.57 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.16), residues: 3035 helix: 1.70 (0.12), residues: 1770 sheet: -1.06 (0.33), residues: 261 loop : 0.28 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2292 TYR 0.022 0.002 TYR A2901 PHE 0.023 0.002 PHE A1870 TRP 0.027 0.002 TRP A2584 HIS 0.009 0.002 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00624 (25142) covalent geometry : angle 0.68904 (34089) hydrogen bonds : bond 0.04666 ( 1424) hydrogen bonds : angle 4.51276 ( 4152) *********************** 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 353 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 0.817 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 1346 MET cc_start: 0.6425 (mmm) cc_final: 0.5688 (ptp) REVERT: A 1669 ASP cc_start: 0.8608 (t0) cc_final: 0.8353 (t0) REVERT: A 1769 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7335 (mmm) REVERT: A 1960 PHE cc_start: 0.8346 (t80) cc_final: 0.7976 (t80) REVERT: A 2053 MET cc_start: 0.8245 (mmt) cc_final: 0.7890 (mmt) REVERT: A 2333 LEU cc_start: 0.6396 (mt) cc_final: 0.6177 (mp) REVERT: A 2361 MET cc_start: 0.8291 (tpp) cc_final: 0.8006 (tpt) REVERT: A 2372 ASP cc_start: 0.8224 (p0) cc_final: 0.7770 (m-30) REVERT: A 2376 ASN cc_start: 0.9064 (m-40) cc_final: 0.8780 (m-40) REVERT: A 2471 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 2535 ILE cc_start: 0.9155 (tt) cc_final: 0.8767 (mt) REVERT: A 2962 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7737 (mmtm) REVERT: A 3005 LEU cc_start: 0.8785 (mt) cc_final: 0.8535 (mt) REVERT: A 3043 MET cc_start: 0.6555 (mpp) cc_final: 0.6290 (mpp) REVERT: A 4095 MET cc_start: 0.8134 (tmm) cc_final: 0.7908 (tmm) REVERT: A 4346 MET cc_start: 0.9076 (mmt) cc_final: 0.8727 (mmt) REVERT: A 4347 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 4473 MET cc_start: 0.8274 (tmm) cc_final: 0.7975 (tmm) outliers start: 54 outliers final: 38 residues processed: 331 average time/residue: 0.1499 time to fit residues: 80.5956 Evaluate side-chains 305 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 1946 VAL 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 2490 ILE 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 2877 LEU Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3143 ILE 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 3702 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU 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 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 145 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 A3057 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** 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 = 0.3744 r_free = 0.3744 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080424 restraints weight = 74306.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082689 restraints weight = 39135.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084101 restraints weight = 26361.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085015 restraints weight = 20787.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085606 restraints weight = 17929.626| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25142 Z= 0.179 Angle : 0.606 11.754 34089 Z= 0.303 Chirality : 0.041 0.206 3821 Planarity : 0.004 0.051 4367 Dihedral : 6.284 86.969 3377 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.92 % Allowed : 11.53 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.16), residues: 3035 helix: 1.79 (0.12), residues: 1767 sheet: -1.30 (0.33), residues: 259 loop : 0.26 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3743 TYR 0.020 0.002 TYR A2748 PHE 0.021 0.002 PHE A2635 TRP 0.024 0.001 TRP A1701 HIS 0.010 0.001 HIS A1559 Details of bonding type rmsd covalent geometry : bond 0.00405 (25142) covalent geometry : angle 0.60569 (34089) hydrogen bonds : bond 0.04150 ( 1424) hydrogen bonds : angle 4.28676 ( 4152) *********************** 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 346 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.956 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: 0.6294 (mmm) cc_final: 0.5785 (ptp) REVERT: A 1507 MET cc_start: 0.5726 (mmm) cc_final: 0.5491 (mmm) REVERT: A 1531 MET cc_start: 0.7963 (tpt) cc_final: 0.7541 (tpt) REVERT: A 1575 PHE cc_start: 0.7406 (t80) cc_final: 0.7166 (t80) REVERT: A 1678 SER cc_start: 0.8920 (t) cc_final: 0.8667 (p) REVERT: A 1769 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: A 1958 ASP cc_start: 0.8191 (t0) cc_final: 0.7977 (t0) REVERT: A 1960 PHE cc_start: 0.8223 (t80) cc_final: 0.7906 (t80) REVERT: A 2053 MET cc_start: 0.8341 (mmt) cc_final: 0.7989 (mmt) REVERT: A 2262 ASP cc_start: 0.8580 (p0) cc_final: 0.8224 (p0) REVERT: A 2333 LEU cc_start: 0.6709 (mt) cc_final: 0.6435 (mp) REVERT: A 2361 MET cc_start: 0.8417 (tpp) cc_final: 0.7959 (tpt) REVERT: A 2372 ASP cc_start: 0.8395 (p0) cc_final: 0.7787 (m-30) REVERT: A 2471 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 2535 ILE cc_start: 0.9230 (tt) cc_final: 0.8870 (mt) REVERT: A 2789 GLN cc_start: 0.8453 (mp10) cc_final: 0.8076 (mp10) REVERT: A 2841 GLU cc_start: 0.8333 (pm20) cc_final: 0.8108 (pm20) REVERT: A 2855 LEU cc_start: 0.9011 (tt) cc_final: 0.8632 (pp) REVERT: A 2962 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7732 (mmtm) REVERT: A 3005 LEU cc_start: 0.8766 (mt) cc_final: 0.8460 (mt) REVERT: A 3026 TYR cc_start: 0.8499 (t80) cc_final: 0.8198 (t80) REVERT: A 3030 MET cc_start: 0.8512 (mmp) cc_final: 0.7989 (mmp) REVERT: A 3633 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8069 (mt) REVERT: A 4007 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8117 (ttp) REVERT: A 4095 MET cc_start: 0.8201 (tmm) cc_final: 0.7938 (tmm) REVERT: A 4346 MET cc_start: 0.9232 (mmt) cc_final: 0.8921 (mmt) REVERT: A 4347 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 4587 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8346 (pp) outliers start: 52 outliers final: 28 residues processed: 326 average time/residue: 0.1479 time to fit residues: 77.2669 Evaluate side-chains 293 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1559 HIS 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 2247 VAL 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 2877 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2939 SER 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 3749 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4587 LEU Chi-restraints excluded: chain A residue 4593 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 238 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN A2187 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN A3092 ASN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3845 ASN A3931 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074378 restraints weight = 75647.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076526 restraints weight = 39909.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077903 restraints weight = 26904.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078735 restraints weight = 21116.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079172 restraints weight = 18241.551| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25142 Z= 0.274 Angle : 0.678 12.031 34089 Z= 0.341 Chirality : 0.043 0.202 3821 Planarity : 0.004 0.052 4367 Dihedral : 6.427 87.970 3377 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.66 % Allowed : 13.38 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.15), residues: 3035 helix: 1.60 (0.12), residues: 1763 sheet: -1.33 (0.32), residues: 268 loop : 0.14 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2977 TYR 0.018 0.002 TYR A3801 PHE 0.033 0.002 PHE A2635 TRP 0.024 0.002 TRP A1701 HIS 0.008 0.001 HIS A1559 Details of bonding type rmsd covalent geometry : bond 0.00616 (25142) covalent geometry : angle 0.67815 (34089) hydrogen bonds : bond 0.04309 ( 1424) hydrogen bonds : angle 4.44728 ( 4152) *********************** 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 339 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 267 time to evaluate : 0.847 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: 0.6220 (mmm) cc_final: 0.5680 (ptp) REVERT: A 1531 MET cc_start: 0.7887 (tpt) cc_final: 0.7451 (tpt) REVERT: A 1589 MET cc_start: 0.6067 (mmm) cc_final: 0.5634 (mmp) REVERT: A 1678 SER cc_start: 0.9029 (t) cc_final: 0.8704 (p) REVERT: A 1769 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7515 (mmm) REVERT: A 1960 PHE cc_start: 0.8401 (t80) cc_final: 0.8074 (t80) REVERT: A 2012 MET cc_start: 0.8309 (tpp) cc_final: 0.7645 (tpp) REVERT: A 2333 LEU cc_start: 0.7062 (mt) cc_final: 0.6650 (mp) REVERT: A 2361 MET cc_start: 0.8475 (tpp) cc_final: 0.8049 (tpt) REVERT: A 2471 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 2535 ILE cc_start: 0.9354 (tt) cc_final: 0.9087 (mt) REVERT: A 2670 ASP cc_start: 0.7659 (p0) cc_final: 0.7420 (p0) REVERT: A 2789 GLN cc_start: 0.8437 (mp10) cc_final: 0.7965 (mp10) REVERT: A 2855 LEU cc_start: 0.8965 (tt) cc_final: 0.8578 (pp) REVERT: A 2962 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7651 (mmtm) REVERT: A 3005 LEU cc_start: 0.8827 (mt) cc_final: 0.8593 (mt) REVERT: A 3885 MET cc_start: 0.8296 (ttm) cc_final: 0.7951 (ttm) REVERT: A 4095 MET cc_start: 0.8298 (tmm) cc_final: 0.7924 (tmm) outliers start: 72 outliers final: 46 residues processed: 321 average time/residue: 0.1453 time to fit residues: 76.3721 Evaluate side-chains 285 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1664 ILE 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 2150 VAL 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 2441 PHE Chi-restraints excluded: chain A residue 2555 ILE 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 2877 LEU Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2915 VAL 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 3075 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3143 ILE 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 3704 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3931 GLN Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4539 LEU Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 LEU Chi-restraints excluded: chain A residue 4593 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 231 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** A3057 GLN A3535 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.104783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077040 restraints weight = 74468.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079314 restraints weight = 38544.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080780 restraints weight = 25678.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081720 restraints weight = 19972.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.082235 restraints weight = 17094.858| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25142 Z= 0.126 Angle : 0.580 9.073 34089 Z= 0.289 Chirality : 0.040 0.181 3821 Planarity : 0.004 0.052 4367 Dihedral : 6.237 84.633 3377 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.92 % Allowed : 15.48 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.16), residues: 3035 helix: 1.88 (0.12), residues: 1760 sheet: -1.33 (0.33), residues: 260 loop : 0.28 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2273 TYR 0.025 0.001 TYR A2748 PHE 0.026 0.002 PHE A1938 TRP 0.022 0.001 TRP A1701 HIS 0.009 0.001 HIS A1559 Details of bonding type rmsd covalent geometry : bond 0.00282 (25142) covalent geometry : angle 0.57977 (34089) hydrogen bonds : bond 0.03873 ( 1424) hydrogen bonds : angle 4.16781 ( 4152) *********************** 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 330 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.906 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: 0.6184 (mmm) cc_final: 0.5775 (ptt) REVERT: A 1472 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 1531 MET cc_start: 0.7727 (tpt) cc_final: 0.7271 (tpt) REVERT: A 1575 PHE cc_start: 0.7256 (t80) cc_final: 0.6852 (t80) REVERT: A 1589 MET cc_start: 0.6146 (mmm) cc_final: 0.5801 (mmp) REVERT: A 1678 SER cc_start: 0.9003 (t) cc_final: 0.8757 (p) REVERT: A 1960 PHE cc_start: 0.8098 (t80) cc_final: 0.7763 (t80) REVERT: A 2012 MET cc_start: 0.8375 (tpp) cc_final: 0.7523 (tpp) REVERT: A 2047 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 2053 MET cc_start: 0.8478 (mmt) cc_final: 0.8061 (mmt) REVERT: A 2333 LEU cc_start: 0.7033 (mt) cc_final: 0.6633 (mp) REVERT: A 2361 MET cc_start: 0.8364 (tpp) cc_final: 0.8063 (tpt) REVERT: A 2471 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 2535 ILE cc_start: 0.9364 (tt) cc_final: 0.9063 (mt) REVERT: A 2789 GLN cc_start: 0.8462 (mp10) cc_final: 0.7960 (mp10) REVERT: A 2855 LEU cc_start: 0.9003 (tt) cc_final: 0.8624 (pp) REVERT: A 2869 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7524 (mmm160) REVERT: A 2962 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7597 (mmtm) REVERT: A 3005 LEU cc_start: 0.8897 (mt) cc_final: 0.8606 (mt) REVERT: A 4078 ASN cc_start: 0.8697 (m110) cc_final: 0.8475 (m-40) REVERT: A 4095 MET cc_start: 0.8242 (tmm) cc_final: 0.7895 (tmm) outliers start: 52 outliers final: 36 residues processed: 313 average time/residue: 0.1387 time to fit residues: 71.0673 Evaluate side-chains 290 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 1811 LEU 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 2441 PHE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 2910 VAL 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 3177 LEU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3818 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 4504 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4539 LEU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2346 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3057 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.077696 restraints weight = 73267.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079794 restraints weight = 38936.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081146 restraints weight = 26325.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081896 restraints weight = 20566.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.082521 restraints weight = 17915.578| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25142 Z= 0.211 Angle : 0.631 10.079 34089 Z= 0.315 Chirality : 0.041 0.184 3821 Planarity : 0.004 0.051 4367 Dihedral : 6.249 85.529 3377 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.62 % Allowed : 16.26 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.16), residues: 3035 helix: 1.81 (0.12), residues: 1761 sheet: -1.41 (0.32), residues: 262 loop : 0.24 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1966 TYR 0.025 0.002 TYR A3026 PHE 0.032 0.002 PHE A2635 TRP 0.023 0.002 TRP A1701 HIS 0.010 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00481 (25142) covalent geometry : angle 0.63091 (34089) hydrogen bonds : bond 0.04013 ( 1424) hydrogen bonds : angle 4.25002 ( 4152) *********************** 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 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: 0.6189 (mmm) cc_final: 0.5824 (ptp) REVERT: A 1472 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 1507 MET cc_start: 0.5437 (mmm) cc_final: 0.5017 (mmm) REVERT: A 1531 MET cc_start: 0.7876 (tpt) cc_final: 0.7364 (tpt) REVERT: A 1579 MET cc_start: 0.8445 (mmm) cc_final: 0.8216 (mmm) REVERT: A 1589 MET cc_start: 0.6348 (mmm) cc_final: 0.5382 (mtp) REVERT: A 1960 PHE cc_start: 0.8221 (t80) cc_final: 0.7944 (t80) REVERT: A 2012 MET cc_start: 0.8161 (tpp) cc_final: 0.7612 (tpp) REVERT: A 2333 LEU cc_start: 0.6905 (mt) cc_final: 0.6506 (mp) REVERT: A 2471 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 2535 ILE cc_start: 0.9295 (tt) cc_final: 0.9086 (mt) REVERT: A 2789 GLN cc_start: 0.8376 (mp10) cc_final: 0.7977 (mp10) REVERT: A 2855 LEU cc_start: 0.8878 (tt) cc_final: 0.8572 (pp) REVERT: A 2962 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7553 (mmtm) REVERT: A 3005 LEU cc_start: 0.8862 (mt) cc_final: 0.8545 (mt) REVERT: A 3516 TYR cc_start: 0.7885 (m-80) cc_final: 0.6305 (m-80) REVERT: A 3570 ASP cc_start: 0.7159 (m-30) cc_final: 0.6870 (m-30) REVERT: A 3885 MET cc_start: 0.8003 (ttm) cc_final: 0.7801 (ttm) REVERT: A 3902 ASP cc_start: 0.8458 (p0) cc_final: 0.8186 (p0) REVERT: A 3938 LEU cc_start: 0.8930 (tp) cc_final: 0.8542 (tp) REVERT: A 4630 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (mt-10) outliers start: 71 outliers final: 47 residues processed: 316 average time/residue: 0.1581 time to fit residues: 80.9742 Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2150 VAL 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 2441 PHE Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2910 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 3704 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3833 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 4338 ASP Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4539 LEU Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4593 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 165 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** A3057 GLN ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** 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 = 0.3761 r_free = 0.3761 target = 0.107586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081752 restraints weight = 71960.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083917 restraints weight = 38363.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085322 restraints weight = 25958.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086223 restraints weight = 20221.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086804 restraints weight = 17378.606| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25142 Z= 0.128 Angle : 0.590 10.112 34089 Z= 0.292 Chirality : 0.040 0.178 3821 Planarity : 0.004 0.051 4367 Dihedral : 6.069 77.980 3377 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.25 % Allowed : 17.33 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.16), residues: 3035 helix: 1.91 (0.12), residues: 1762 sheet: -1.35 (0.33), residues: 257 loop : 0.31 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2273 TYR 0.023 0.001 TYR A2748 PHE 0.056 0.002 PHE A4410 TRP 0.021 0.001 TRP A1701 HIS 0.010 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00289 (25142) covalent geometry : angle 0.58957 (34089) hydrogen bonds : bond 0.03769 ( 1424) hydrogen bonds : angle 4.11454 ( 4152) *********************** 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 337 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 1507 MET cc_start: 0.5306 (mmm) cc_final: 0.4977 (mmm) REVERT: A 1531 MET cc_start: 0.7872 (tpt) cc_final: 0.7354 (tpt) REVERT: A 1575 PHE cc_start: 0.7185 (t80) cc_final: 0.6783 (t80) REVERT: A 1587 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5853 (tp) REVERT: A 1589 MET cc_start: 0.6281 (mmm) cc_final: 0.5347 (mtm) REVERT: A 1960 PHE cc_start: 0.8018 (t80) cc_final: 0.7759 (t80) REVERT: A 2012 MET cc_start: 0.8190 (tpp) cc_final: 0.7503 (tpp) REVERT: A 2047 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 2053 MET cc_start: 0.8409 (mmt) cc_final: 0.8047 (mmt) REVERT: A 2145 MET cc_start: 0.8305 (tpp) cc_final: 0.8013 (mmt) REVERT: A 2333 LEU cc_start: 0.6841 (mt) cc_final: 0.6463 (mp) REVERT: A 2471 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 2789 GLN cc_start: 0.8418 (mp10) cc_final: 0.7996 (mp10) REVERT: A 2855 LEU cc_start: 0.8916 (tt) cc_final: 0.8610 (pp) REVERT: A 2962 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7528 (mmtm) REVERT: A 2975 ASP cc_start: 0.8853 (m-30) cc_final: 0.8540 (p0) REVERT: A 3005 LEU cc_start: 0.8834 (mt) cc_final: 0.8550 (mt) REVERT: A 3570 ASP cc_start: 0.7156 (m-30) cc_final: 0.6902 (m-30) REVERT: A 3902 ASP cc_start: 0.8442 (p0) cc_final: 0.8235 (p0) REVERT: A 3938 LEU cc_start: 0.8959 (tp) cc_final: 0.8575 (tp) REVERT: A 4078 ASN cc_start: 0.8564 (m-40) cc_final: 0.8235 (p0) REVERT: A 4410 PHE cc_start: 0.7742 (t80) cc_final: 0.7455 (t80) REVERT: A 4587 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8475 (pp) REVERT: A 4630 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7726 (mm-30) outliers start: 61 outliers final: 42 residues processed: 322 average time/residue: 0.1493 time to fit residues: 78.3056 Evaluate side-chains 292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 1587 LEU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1968 LEU 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 2441 PHE Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2915 VAL 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 3089 CYS Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3177 LEU 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 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3862 ASP 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 4448 LEU Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4539 LEU Chi-restraints excluded: chain A residue 4587 LEU Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 199 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 237 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2322 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.108079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082219 restraints weight = 72549.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084427 restraints weight = 38542.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085833 restraints weight = 25960.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086708 restraints weight = 20384.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087166 restraints weight = 17531.825| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25142 Z= 0.118 Angle : 0.602 10.876 34089 Z= 0.297 Chirality : 0.040 0.239 3821 Planarity : 0.004 0.050 4367 Dihedral : 5.874 67.207 3377 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.29 % Allowed : 17.66 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.16), residues: 3035 helix: 1.98 (0.12), residues: 1766 sheet: -1.33 (0.33), residues: 263 loop : 0.33 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2729 TYR 0.022 0.001 TYR A2748 PHE 0.036 0.001 PHE A4410 TRP 0.021 0.001 TRP A1701 HIS 0.011 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00261 (25142) covalent geometry : angle 0.60182 (34089) hydrogen bonds : bond 0.03628 ( 1424) hydrogen bonds : angle 4.03315 ( 4152) *********************** 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 347 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 1507 MET cc_start: 0.5195 (mmm) cc_final: 0.4929 (mmm) REVERT: A 1531 MET cc_start: 0.7727 (tpt) cc_final: 0.7241 (tpt) REVERT: A 1575 PHE cc_start: 0.7163 (t80) cc_final: 0.6915 (t80) REVERT: A 1587 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5753 (tp) REVERT: A 1589 MET cc_start: 0.6329 (mmm) cc_final: 0.5396 (mtm) REVERT: A 1960 PHE cc_start: 0.7901 (t80) cc_final: 0.7618 (t80) REVERT: A 2012 MET cc_start: 0.8168 (tpp) cc_final: 0.7435 (tpp) REVERT: A 2047 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 2053 MET cc_start: 0.8354 (mmt) cc_final: 0.7967 (mmt) REVERT: A 2145 MET cc_start: 0.8316 (tpp) cc_final: 0.8035 (mmt) REVERT: A 2333 LEU cc_start: 0.6801 (mt) cc_final: 0.6558 (mp) REVERT: A 2471 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 2584 TRP cc_start: 0.8357 (m-10) cc_final: 0.7980 (m-10) REVERT: A 2712 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6607 (t) REVERT: A 2837 LEU cc_start: 0.8900 (mt) cc_final: 0.8473 (mp) REVERT: A 2855 LEU cc_start: 0.8927 (tt) cc_final: 0.8613 (pp) REVERT: A 2869 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7071 (mmt180) REVERT: A 2975 ASP cc_start: 0.8861 (m-30) cc_final: 0.8552 (p0) REVERT: A 3002 SER cc_start: 0.8612 (m) cc_final: 0.8270 (p) REVERT: A 3005 LEU cc_start: 0.8784 (mt) cc_final: 0.8547 (mt) REVERT: A 3008 MET cc_start: 0.9060 (mmm) cc_final: 0.8788 (tpp) REVERT: A 3078 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.8214 (tpp-160) REVERT: A 3570 ASP cc_start: 0.7168 (m-30) cc_final: 0.6957 (m-30) REVERT: A 4078 ASN cc_start: 0.8612 (m-40) cc_final: 0.8277 (p0) REVERT: A 4343 MET cc_start: 0.9188 (ttm) cc_final: 0.8248 (ttm) REVERT: A 4630 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7697 (mm-30) outliers start: 62 outliers final: 47 residues processed: 326 average time/residue: 0.1519 time to fit residues: 80.6687 Evaluate side-chains 308 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 1587 LEU 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 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 2441 PHE Chi-restraints excluded: chain A residue 2555 ILE 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 2686 MET Chi-restraints excluded: chain A residue 2712 CYS Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2939 SER 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 3043 MET Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3177 LEU 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 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3862 ASP 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 4448 LEU Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4479 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4539 LEU Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 189 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3880 HIS ** 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 = 0.3722 r_free = 0.3722 target = 0.105220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078833 restraints weight = 73990.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080918 restraints weight = 40729.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082262 restraints weight = 28144.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083127 restraints weight = 22380.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083657 restraints weight = 19526.881| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25142 Z= 0.217 Angle : 0.654 11.080 34089 Z= 0.327 Chirality : 0.042 0.185 3821 Planarity : 0.004 0.051 4367 Dihedral : 5.938 64.705 3377 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 17.78 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 3035 helix: 1.86 (0.12), residues: 1764 sheet: -1.36 (0.33), residues: 266 loop : 0.29 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1621 TYR 0.023 0.002 TYR A3026 PHE 0.055 0.002 PHE A4410 TRP 0.022 0.002 TRP A1701 HIS 0.013 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00493 (25142) covalent geometry : angle 0.65450 (34089) hydrogen bonds : bond 0.03878 ( 1424) hydrogen bonds : angle 4.19476 ( 4152) *********************** 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 320 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (p) REVERT: A 1507 MET cc_start: 0.5386 (mmm) cc_final: 0.5096 (mmm) REVERT: A 1531 MET cc_start: 0.7767 (tpt) cc_final: 0.7259 (tpt) REVERT: A 1587 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5817 (tt) REVERT: A 1589 MET cc_start: 0.6340 (mmm) cc_final: 0.5397 (mtm) REVERT: A 1938 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 1960 PHE cc_start: 0.8040 (t80) cc_final: 0.7831 (t80) REVERT: A 2012 MET cc_start: 0.8201 (tpp) cc_final: 0.7701 (tpp) REVERT: A 2053 MET cc_start: 0.8319 (mmt) cc_final: 0.7971 (mmt) REVERT: A 2145 MET cc_start: 0.8303 (tpp) cc_final: 0.8100 (mmt) REVERT: A 2333 LEU cc_start: 0.7006 (mt) cc_final: 0.6662 (mp) REVERT: A 2471 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 2789 GLN cc_start: 0.8384 (mp10) cc_final: 0.8023 (mp10) REVERT: A 2837 LEU cc_start: 0.9011 (mt) cc_final: 0.8614 (mp) REVERT: A 2855 LEU cc_start: 0.8848 (tt) cc_final: 0.8552 (pp) REVERT: A 3002 SER cc_start: 0.8490 (m) cc_final: 0.8185 (p) REVERT: A 3008 MET cc_start: 0.9030 (mmm) cc_final: 0.8776 (tpp) REVERT: A 3078 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.8120 (tpp-160) REVERT: A 3570 ASP cc_start: 0.6878 (m-30) cc_final: 0.6660 (m-30) REVERT: A 3938 LEU cc_start: 0.8967 (tp) cc_final: 0.8581 (tp) REVERT: A 4078 ASN cc_start: 0.8525 (m-40) cc_final: 0.8184 (p0) REVERT: A 4410 PHE cc_start: 0.7752 (t80) cc_final: 0.7511 (t80) REVERT: A 4473 MET cc_start: 0.8563 (tpt) cc_final: 0.8206 (tpt) REVERT: A 4630 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7691 (mt-10) outliers start: 67 outliers final: 47 residues processed: 303 average time/residue: 0.1518 time to fit residues: 75.3723 Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 1587 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 1938 PHE Chi-restraints excluded: chain A residue 2039 LEU 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 2250 VAL Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2555 ILE 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 2686 MET Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2939 SER 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 3043 MET Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3610 THR 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 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3862 ASP 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 4448 LEU Chi-restraints excluded: chain A residue 4476 ILE 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 4630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 230 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 242 optimal weight: 0.6980 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1939 GLN A2171 HIS ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083895 restraints weight = 70263.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085990 restraints weight = 38429.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087307 restraints weight = 26703.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088127 restraints weight = 21470.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088495 restraints weight = 18883.647| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25142 Z= 0.128 Angle : 0.635 11.160 34089 Z= 0.314 Chirality : 0.041 0.185 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.694 58.302 3377 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.96 % Allowed : 18.81 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.16), residues: 3035 helix: 1.92 (0.12), residues: 1766 sheet: -1.35 (0.33), residues: 260 loop : 0.25 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1621 TYR 0.023 0.001 TYR A3519 PHE 0.038 0.002 PHE A4410 TRP 0.022 0.001 TRP A1701 HIS 0.013 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00288 (25142) covalent geometry : angle 0.63458 (34089) hydrogen bonds : bond 0.03722 ( 1424) hydrogen bonds : angle 4.10941 ( 4152) ********************** 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 312 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7759 (p) REVERT: A 1507 MET cc_start: 0.5280 (mmm) cc_final: 0.4967 (mmm) REVERT: A 1531 MET cc_start: 0.7668 (tpt) cc_final: 0.7159 (tpt) REVERT: A 1587 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5741 (tt) REVERT: A 1589 MET cc_start: 0.6312 (mmm) cc_final: 0.5363 (mtm) REVERT: A 1960 PHE cc_start: 0.8045 (t80) cc_final: 0.7809 (t80) REVERT: A 2012 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7689 (tpp) REVERT: A 2053 MET cc_start: 0.8384 (mmt) cc_final: 0.8018 (mmt) REVERT: A 2145 MET cc_start: 0.8415 (tpp) cc_final: 0.8112 (mmt) REVERT: A 2333 LEU cc_start: 0.7067 (mt) cc_final: 0.6709 (mp) REVERT: A 2471 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 2510 MET cc_start: 0.7564 (ttm) cc_final: 0.7348 (ttm) REVERT: A 2584 TRP cc_start: 0.8397 (m-10) cc_final: 0.8170 (m-10) REVERT: A 2789 GLN cc_start: 0.8513 (mp10) cc_final: 0.8063 (mp10) REVERT: A 2837 LEU cc_start: 0.8922 (mt) cc_final: 0.8480 (mp) REVERT: A 2855 LEU cc_start: 0.8925 (tt) cc_final: 0.8571 (pp) REVERT: A 3002 SER cc_start: 0.8773 (m) cc_final: 0.8451 (p) REVERT: A 3008 MET cc_start: 0.9164 (mmm) cc_final: 0.8896 (tpp) REVERT: A 3938 LEU cc_start: 0.8987 (tp) cc_final: 0.8614 (tp) REVERT: A 4078 ASN cc_start: 0.8752 (m-40) cc_final: 0.8344 (p0) REVERT: A 4630 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (mm-30) outliers start: 53 outliers final: 37 residues processed: 299 average time/residue: 0.1507 time to fit residues: 73.6950 Evaluate side-chains 285 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 1587 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 2012 MET Chi-restraints excluded: chain A residue 2039 LEU 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 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 2686 MET Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2877 LEU 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 3177 LEU Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3862 ASP 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 4448 LEU 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 4630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 33 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 97 optimal weight: 0.0370 chunk 193 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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** A3047 HIS ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN A3880 HIS 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 = 0.3753 r_free = 0.3753 target = 0.106948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080527 restraints weight = 73770.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082733 restraints weight = 38995.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084155 restraints weight = 26340.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085078 restraints weight = 20653.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085679 restraints weight = 17751.867| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25142 Z= 0.135 Angle : 0.635 10.922 34089 Z= 0.315 Chirality : 0.041 0.184 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.535 57.803 3377 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.81 % Allowed : 18.92 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.16), residues: 3035 helix: 1.90 (0.12), residues: 1776 sheet: -1.35 (0.33), residues: 257 loop : 0.22 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2285 TYR 0.028 0.001 TYR A3026 PHE 0.041 0.002 PHE A4410 TRP 0.026 0.001 TRP A2363 HIS 0.012 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00309 (25142) covalent geometry : angle 0.63504 (34089) hydrogen bonds : bond 0.03696 ( 1424) hydrogen bonds : angle 4.09512 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4252.85 seconds wall clock time: 74 minutes 24.79 seconds (4464.79 seconds total)