Starting phenix.real_space_refine on Sat May 24 02:27:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmc_44695/05_2025/9bmc_44695.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.029 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 2 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 32 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24617 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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 13.71, per 1000 atoms: 0.56 Number of scatterers: 24617 At special positions: 0 Unit cell: (127.303, 170.123, 185.168, 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 2 11.99 O 4584 8.00 N 4254 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 19 sheets defined 63.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1350 through 1354 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: 3.618A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1472 Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.723A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1515 removed outlier: 5.180A pdb=" N TYR A1512 " --> pdb=" O LEU A1509 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.517A pdb=" N ALA A1520 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.644A pdb=" N LEU A1561 " --> pdb=" O ILE A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 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 1646 through 1652 removed outlier: 3.610A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.518A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.661A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1773 removed outlier: 3.570A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.669A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.564A 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 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.694A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 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: 3.669A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.165A 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 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.525A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 4.129A 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 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.811A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.580A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) 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 2586 Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.955A 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 2739 through 2757 removed outlier: 4.284A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2761 through 2764 removed outlier: 4.078A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2761 through 2764' Processing helix chain 'A' and resid 2765 through 2782 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 4.013A 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 2839 through 2858 removed outlier: 3.767A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) removed outlier: 3.562A 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 Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.655A pdb=" N LEU A2920 " --> pdb=" O LEU A2916 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.608A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3002 through 3015 removed outlier: 3.990A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.528A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 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: 3.662A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.870A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.419A 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 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 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 3650 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3706 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 4.190A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.283A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 removed outlier: 3.550A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) 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 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.002A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3952 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.977A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 removed outlier: 3.950A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4014 through 4017 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.618A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.933A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.977A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 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 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 4.111A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.525A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4252 through 4256 removed outlier: 3.944A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) 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 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 3.998A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.784A 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 4532 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 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.364A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 7.931A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.673A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (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: 6.116A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.507A 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: 6.914A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 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 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2617 removed outlier: 6.714A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.635A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.366A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.263A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.470A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A4128 " --> pdb=" O MET A4043 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG A4143 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS A4044 " --> pdb=" O ARG A4143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.959A 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: 6.278A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.978A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1445 hydrogen bonds defined for protein. 4197 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: 16.84 Time building geometry restraints manager: 7.33 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: 8112 1.34 - 1.46: 4630 1.46 - 1.58: 12182 1.58 - 1.70: 12 1.70 - 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 1.495 -0.033 1.17e-02 7.31e+03 8.17e+00 bond pdb=" N PHE A1568 " pdb=" CA PHE A1568 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.68e+00 bond pdb=" N LEU A1607 " pdb=" CA LEU A1607 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.54e+00 bond pdb=" N LEU A1608 " pdb=" CA LEU A1608 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" N SER A1570 " pdb=" CA SER A1570 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.14e+00 ... (remaining 25137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 33551 2.01 - 4.01: 463 4.01 - 6.02: 66 6.02 - 8.02: 7 8.02 - 10.03: 2 Bond angle restraints: 34089 Sorted by residual: angle pdb=" N MET A1457 " pdb=" CA MET A1457 " pdb=" CB MET A1457 " ideal model delta sigma weight residual 110.30 116.93 -6.63 1.54e+00 4.22e-01 1.85e+01 angle pdb=" C GLU A1456 " pdb=" N MET A1457 " pdb=" CA MET A1457 " ideal model delta sigma weight residual 120.68 114.35 6.33 1.70e+00 3.46e-01 1.39e+01 angle pdb=" CB MET A1457 " pdb=" CG MET A1457 " pdb=" SD MET A1457 " ideal model delta sigma weight residual 112.70 122.73 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA THR A1565 " pdb=" CB THR A1565 " pdb=" OG1 THR A1565 " ideal model delta sigma weight residual 109.60 104.86 4.74 1.50e+00 4.44e-01 9.98e+00 angle pdb=" CA MET A1457 " pdb=" CB MET A1457 " pdb=" CG MET A1457 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.13e+00 ... (remaining 34084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 13607 17.72 - 35.45: 1343 35.45 - 53.17: 201 53.17 - 70.90: 81 70.90 - 88.62: 26 Dihedral angle restraints: 15258 sinusoidal: 6348 harmonic: 8910 Sorted by residual: 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 -132.72 72.72 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA TRP A3093 " pdb=" C TRP A3093 " pdb=" N PHE A3094 " pdb=" CA PHE A3094 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP A2262 " pdb=" CB ASP A2262 " pdb=" CG ASP A2262 " pdb=" OD1 ASP A2262 " ideal model delta sinusoidal sigma weight residual -30.00 -88.24 58.24 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2842 0.041 - 0.083: 727 0.083 - 0.124: 232 0.124 - 0.165: 17 0.165 - 0.207: 3 Chirality restraints: 3821 Sorted by residual: chirality pdb=" CG LEU A2581 " pdb=" CB LEU A2581 " pdb=" CD1 LEU A2581 " pdb=" CD2 LEU A2581 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A1611 " pdb=" N ILE A1611 " pdb=" C ILE A1611 " pdb=" CB ILE A1611 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A4027 " pdb=" CB LEU A4027 " pdb=" CD1 LEU A4027 " pdb=" CD2 LEU A4027 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 3818 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A2907 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A2908 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A2908 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A2908 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A4023 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A4024 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A4024 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A4024 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A2773 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C MET A2773 " -0.032 2.00e-02 2.50e+03 pdb=" O MET A2773 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A2774 " 0.011 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 119 2.50 - 3.10: 18296 3.10 - 3.70: 38289 3.70 - 4.30: 53078 4.30 - 4.90: 89677 Nonbonded interactions: 199459 Sorted by model distance: nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4706 " model vdw 1.903 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 2.039 2.170 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR A3103 " pdb=" OE1 GLU A3141 " model vdw 2.150 3.040 nonbonded pdb=" NZ LYS A4505 " pdb=" O ASP A4554 " model vdw 2.167 3.120 ... (remaining 199454 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: 3.150 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: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 63.380 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25142 Z= 0.171 Angle : 0.580 10.026 34089 Z= 0.302 Chirality : 0.040 0.207 3821 Planarity : 0.004 0.072 4367 Dihedral : 14.794 88.619 9470 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 0.04 % Allowed : 0.55 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 3035 helix: 1.74 (0.13), residues: 1768 sheet: -0.90 (0.32), residues: 259 loop : 0.34 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3489 HIS 0.007 0.001 HIS A3155 PHE 0.021 0.002 PHE A1626 TYR 0.022 0.001 TYR A1546 ARG 0.005 0.000 ARG A2869 Details of bonding type rmsd hydrogen bonds : bond 0.12605 ( 1445) hydrogen bonds : angle 5.51991 ( 4197) covalent geometry : bond 0.00377 (25142) covalent geometry : angle 0.57989 (34089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 3.108 Fit side-chains revert: symmetry clash REVERT: A 2189 MET cc_start: 0.8538 (ptm) cc_final: 0.8297 (ptm) REVERT: A 2639 CYS cc_start: 0.6874 (m) cc_final: 0.6654 (m) REVERT: A 2767 GLU cc_start: 0.7081 (tp30) cc_final: 0.6813 (tp30) REVERT: A 3663 THR cc_start: 0.8607 (p) cc_final: 0.7841 (p) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.3713 time to fit residues: 178.3961 Evaluate side-chains 239 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2212 GLN A3092 ASN ** A3865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104842 restraints weight = 39002.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108147 restraints weight = 24015.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108883 restraints weight = 15625.171| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25142 Z= 0.129 Angle : 0.528 10.108 34089 Z= 0.265 Chirality : 0.039 0.175 3821 Planarity : 0.004 0.057 4367 Dihedral : 5.606 71.223 3377 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % Rotamer: Outliers : 0.85 % Allowed : 6.69 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 3035 helix: 2.09 (0.12), residues: 1784 sheet: -0.84 (0.33), residues: 248 loop : 0.41 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1523 HIS 0.004 0.001 HIS A4389 PHE 0.017 0.001 PHE A2992 TYR 0.019 0.001 TYR A1546 ARG 0.006 0.000 ARG A2869 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 1445) hydrogen bonds : angle 4.29599 ( 4197) covalent geometry : bond 0.00293 (25142) covalent geometry : angle 0.52805 (34089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 3059 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 3068 MET cc_start: 0.6727 (mmt) cc_final: 0.6263 (mmt) REVERT: A 3776 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 4095 MET cc_start: 0.8153 (tpp) cc_final: 0.7777 (tpt) REVERT: A 4346 MET cc_start: 0.8237 (mmm) cc_final: 0.7980 (mmm) REVERT: A 4473 MET cc_start: 0.8048 (ttt) cc_final: 0.7715 (ttt) outliers start: 23 outliers final: 15 residues processed: 290 average time/residue: 0.3533 time to fit residues: 163.9775 Evaluate side-chains 271 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR 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 163 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 224 optimal weight: 0.0970 chunk 198 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A1699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A3092 ASN ** A3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107165 restraints weight = 40409.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107487 restraints weight = 27657.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.108351 restraints weight = 20368.203| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25142 Z= 0.120 Angle : 0.503 10.553 34089 Z= 0.249 Chirality : 0.039 0.187 3821 Planarity : 0.004 0.048 4367 Dihedral : 5.488 78.628 3377 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 1.22 % Allowed : 9.02 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 3035 helix: 2.21 (0.12), residues: 1783 sheet: -0.81 (0.33), residues: 243 loop : 0.41 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.005 0.001 HIS A3534 PHE 0.015 0.001 PHE A3813 TYR 0.017 0.001 TYR A2193 ARG 0.004 0.000 ARG A3775 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1445) hydrogen bonds : angle 4.10360 ( 4197) covalent geometry : bond 0.00274 (25142) covalent geometry : angle 0.50332 (34089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 2.733 Fit side-chains revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0025 (tpt) cc_final: -0.2990 (mtt) REVERT: A 1488 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6849 (mtm-85) REVERT: A 1892 MET cc_start: 0.9017 (mmp) cc_final: 0.8809 (mmp) REVERT: A 2479 PHE cc_start: 0.7330 (m-80) cc_final: 0.7059 (m-80) REVERT: A 3059 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 3551 GLU cc_start: 0.7006 (mp0) cc_final: 0.6670 (mp0) REVERT: A 3776 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: A 4346 MET cc_start: 0.8498 (mmm) cc_final: 0.8213 (mmm) REVERT: A 4473 MET cc_start: 0.8042 (ttt) cc_final: 0.7720 (ttt) REVERT: A 4646 GLU cc_start: 0.6196 (tt0) cc_final: 0.5851 (tt0) outliers start: 33 outliers final: 20 residues processed: 284 average time/residue: 0.3689 time to fit residues: 168.2142 Evaluate side-chains 274 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4552 THR 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 195 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 292 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A4404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102566 restraints weight = 39519.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104709 restraints weight = 22001.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105887 restraints weight = 15804.625| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25142 Z= 0.187 Angle : 0.554 9.623 34089 Z= 0.277 Chirality : 0.041 0.203 3821 Planarity : 0.004 0.048 4367 Dihedral : 5.534 81.727 3377 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 1.77 % Allowed : 10.01 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 3035 helix: 2.10 (0.12), residues: 1780 sheet: -0.95 (0.33), residues: 243 loop : 0.31 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A3535 PHE 0.021 0.002 PHE A3813 TYR 0.023 0.001 TYR A2193 ARG 0.003 0.000 ARG A3174 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1445) hydrogen bonds : angle 4.10915 ( 4197) covalent geometry : bond 0.00454 (25142) covalent geometry : angle 0.55444 (34089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6583 (mtm-85) REVERT: A 1527 LEU cc_start: 0.6860 (mt) cc_final: 0.6577 (tt) REVERT: A 2012 MET cc_start: 0.8453 (tmm) cc_final: 0.8224 (tmm) REVERT: A 2479 PHE cc_start: 0.7416 (m-80) cc_final: 0.7142 (m-80) REVERT: A 2505 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 3059 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 3489 TRP cc_start: 0.5505 (OUTLIER) cc_final: 0.5121 (m-10) REVERT: A 3661 LEU cc_start: 0.8792 (mm) cc_final: 0.8430 (tp) REVERT: A 3771 GLU cc_start: 0.7351 (pt0) cc_final: 0.7049 (pt0) REVERT: A 3775 ARG cc_start: 0.8593 (ptp90) cc_final: 0.8314 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 4343 MET cc_start: 0.8201 (ttp) cc_final: 0.7893 (ttp) REVERT: A 4346 MET cc_start: 0.8223 (mmm) cc_final: 0.7717 (mmm) REVERT: A 4473 MET cc_start: 0.8235 (ttt) cc_final: 0.7985 (ttt) REVERT: A 4629 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7517 (ptmt) REVERT: A 4646 GLU cc_start: 0.6664 (tt0) cc_final: 0.6351 (tt0) outliers start: 48 outliers final: 33 residues processed: 299 average time/residue: 0.3899 time to fit residues: 185.5288 Evaluate side-chains 292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1597 VAL Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2442 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3724 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR 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 99 optimal weight: 0.0870 chunk 287 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 260 optimal weight: 0.5980 chunk 272 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1699 ASN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2416 GLN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN ** A4466 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.138318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103805 restraints weight = 38828.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106111 restraints weight = 23570.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107632 restraints weight = 15332.747| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25142 Z= 0.114 Angle : 0.504 11.022 34089 Z= 0.249 Chirality : 0.038 0.195 3821 Planarity : 0.003 0.044 4367 Dihedral : 5.408 81.034 3377 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 11.35 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 3035 helix: 2.29 (0.12), residues: 1782 sheet: -0.89 (0.33), residues: 243 loop : 0.36 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A1500 PHE 0.017 0.001 PHE A3813 TYR 0.016 0.001 TYR A2748 ARG 0.009 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1445) hydrogen bonds : angle 3.94505 ( 4197) covalent geometry : bond 0.00260 (25142) covalent geometry : angle 0.50420 (34089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6545 (mtm-85) REVERT: A 1527 LEU cc_start: 0.6973 (mt) cc_final: 0.6721 (tt) REVERT: A 2415 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7569 (tp) REVERT: A 2505 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 3059 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 3489 TRP cc_start: 0.5625 (OUTLIER) cc_final: 0.5255 (m-10) REVERT: A 3725 ASP cc_start: 0.7768 (t0) cc_final: 0.7554 (t70) REVERT: A 3771 GLU cc_start: 0.7431 (pt0) cc_final: 0.7065 (pt0) REVERT: A 3775 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8160 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: A 4343 MET cc_start: 0.8250 (ttp) cc_final: 0.7955 (ttp) REVERT: A 4346 MET cc_start: 0.8239 (mmm) cc_final: 0.7960 (mmm) REVERT: A 4473 MET cc_start: 0.8218 (ttt) cc_final: 0.7980 (ttt) REVERT: A 4629 LYS cc_start: 0.7831 (ptmt) cc_final: 0.7587 (ptmt) REVERT: A 4646 GLU cc_start: 0.6586 (tt0) cc_final: 0.6274 (tt0) outliers start: 49 outliers final: 31 residues processed: 306 average time/residue: 0.3638 time to fit residues: 178.3922 Evaluate side-chains 292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2442 GLN Chi-restraints excluded: chain A residue 2501 SER Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 168 optimal weight: 0.0370 chunk 245 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 180 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A3700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102447 restraints weight = 39131.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105588 restraints weight = 22107.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107009 restraints weight = 14710.549| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1490 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= 0.134 Angle : 0.515 12.085 34089 Z= 0.253 Chirality : 0.039 0.195 3821 Planarity : 0.003 0.044 4367 Dihedral : 5.403 83.021 3377 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 2.07 % Allowed : 11.90 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 3035 helix: 2.29 (0.12), residues: 1784 sheet: -0.94 (0.32), residues: 243 loop : 0.39 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.003 0.001 HIS A3822 PHE 0.018 0.001 PHE A3813 TYR 0.020 0.001 TYR A1546 ARG 0.004 0.000 ARG A3007 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 1445) hydrogen bonds : angle 3.92086 ( 4197) covalent geometry : bond 0.00316 (25142) covalent geometry : angle 0.51481 (34089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0283 (tpt) cc_final: -0.3205 (mtt) REVERT: A 1527 LEU cc_start: 0.6849 (mt) cc_final: 0.6587 (tt) REVERT: A 1973 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: A 2286 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7950 (tppt) REVERT: A 2415 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7522 (tp) REVERT: A 2505 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: A 3059 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 3489 TRP cc_start: 0.5584 (OUTLIER) cc_final: 0.5239 (m-10) REVERT: A 3771 GLU cc_start: 0.7520 (pt0) cc_final: 0.7154 (pt0) REVERT: A 3775 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8142 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 4343 MET cc_start: 0.8229 (ttp) cc_final: 0.7876 (ttp) REVERT: A 4346 MET cc_start: 0.8256 (mmm) cc_final: 0.7988 (mmm) REVERT: A 4473 MET cc_start: 0.8222 (ttt) cc_final: 0.7897 (ttt) REVERT: A 4629 LYS cc_start: 0.7861 (ptmt) cc_final: 0.7610 (ptmt) REVERT: A 4646 GLU cc_start: 0.6589 (tt0) cc_final: 0.6287 (tt0) outliers start: 56 outliers final: 38 residues processed: 313 average time/residue: 0.3550 time to fit residues: 177.7956 Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2501 SER Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 157 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1939 GLN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2781 GLN A2849 ASN A3092 ASN A3535 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102164 restraints weight = 39321.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105722 restraints weight = 23496.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106646 restraints weight = 15083.775| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25142 Z= 0.143 Angle : 0.530 12.093 34089 Z= 0.260 Chirality : 0.040 0.196 3821 Planarity : 0.004 0.049 4367 Dihedral : 5.420 83.560 3377 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 2.14 % Allowed : 12.49 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 3035 helix: 2.29 (0.12), residues: 1781 sheet: -0.99 (0.32), residues: 243 loop : 0.38 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.003 0.001 HIS A3200 PHE 0.019 0.001 PHE A3813 TYR 0.015 0.001 TYR A2496 ARG 0.014 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1445) hydrogen bonds : angle 3.91731 ( 4197) covalent geometry : bond 0.00340 (25142) covalent geometry : angle 0.53046 (34089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0138 (tpt) cc_final: -0.3044 (mtt) REVERT: A 1398 MET cc_start: 0.6745 (tpp) cc_final: 0.6337 (ptt) REVERT: A 1527 LEU cc_start: 0.6898 (mt) cc_final: 0.6656 (tt) REVERT: A 1541 GLN cc_start: 0.7139 (tt0) cc_final: 0.6755 (tt0) REVERT: A 1973 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: A 2187 GLN cc_start: 0.8263 (tp40) cc_final: 0.7992 (tp-100) REVERT: A 2286 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7971 (tppt) REVERT: A 2415 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7573 (tp) REVERT: A 2505 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 3007 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7528 (mtp85) REVERT: A 3059 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 3479 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5993 (mp) REVERT: A 3489 TRP cc_start: 0.5670 (OUTLIER) cc_final: 0.5323 (m-10) REVERT: A 3652 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7337 (pp20) REVERT: A 3771 GLU cc_start: 0.7474 (pt0) cc_final: 0.7131 (pt0) REVERT: A 3775 ARG cc_start: 0.8481 (ptp90) cc_final: 0.8134 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 4343 MET cc_start: 0.8244 (ttp) cc_final: 0.7909 (ttp) REVERT: A 4346 MET cc_start: 0.8310 (mmm) cc_final: 0.7814 (mmm) REVERT: A 4473 MET cc_start: 0.8308 (ttt) cc_final: 0.8002 (ttt) REVERT: A 4629 LYS cc_start: 0.7885 (ptmt) cc_final: 0.7626 (ptmt) REVERT: A 4646 GLU cc_start: 0.6626 (tt0) cc_final: 0.6319 (tt0) outliers start: 58 outliers final: 39 residues processed: 303 average time/residue: 0.3705 time to fit residues: 178.7617 Evaluate side-chains 298 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1597 VAL Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2501 SER Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 114 optimal weight: 0.1980 chunk 130 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 270 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A3535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103009 restraints weight = 39410.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106676 restraints weight = 23577.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107534 restraints weight = 15275.464| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25142 Z= 0.116 Angle : 0.523 12.701 34089 Z= 0.255 Chirality : 0.039 0.201 3821 Planarity : 0.003 0.045 4367 Dihedral : 5.381 84.487 3377 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.70 % Allowed : 13.38 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 3035 helix: 2.36 (0.12), residues: 1783 sheet: -0.93 (0.32), residues: 248 loop : 0.44 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.003 0.001 HIS A3822 PHE 0.017 0.001 PHE A3813 TYR 0.021 0.001 TYR A1546 ARG 0.012 0.000 ARG A1467 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 1445) hydrogen bonds : angle 3.85624 ( 4197) covalent geometry : bond 0.00268 (25142) covalent geometry : angle 0.52279 (34089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0038 (tpt) cc_final: -0.2911 (mtt) REVERT: A 1527 LEU cc_start: 0.6872 (mt) cc_final: 0.6631 (tt) REVERT: A 1541 GLN cc_start: 0.7089 (tt0) cc_final: 0.6709 (tt0) REVERT: A 1892 MET cc_start: 0.9007 (mmp) cc_final: 0.8782 (mmp) REVERT: A 1973 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: A 2187 GLN cc_start: 0.8110 (tp40) cc_final: 0.7908 (tp-100) REVERT: A 2286 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7959 (tppt) REVERT: A 2415 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7523 (tp) REVERT: A 2505 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 3059 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 3479 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5856 (mp) REVERT: A 3489 TRP cc_start: 0.5594 (OUTLIER) cc_final: 0.5228 (m-10) REVERT: A 3661 LEU cc_start: 0.8634 (mm) cc_final: 0.8334 (tp) REVERT: A 3771 GLU cc_start: 0.7448 (pt0) cc_final: 0.7106 (pt0) REVERT: A 3775 ARG cc_start: 0.8500 (ptp90) cc_final: 0.8162 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: A 3910 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: A 4343 MET cc_start: 0.8208 (ttp) cc_final: 0.7875 (ttp) REVERT: A 4344 LEU cc_start: 0.8922 (tp) cc_final: 0.8708 (tp) REVERT: A 4346 MET cc_start: 0.8289 (mmm) cc_final: 0.7825 (mmm) REVERT: A 4473 MET cc_start: 0.8346 (ttt) cc_final: 0.8047 (ttt) REVERT: A 4629 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7631 (ptmt) REVERT: A 4646 GLU cc_start: 0.6682 (tt0) cc_final: 0.6383 (tt0) outliers start: 46 outliers final: 36 residues processed: 297 average time/residue: 0.3498 time to fit residues: 166.9907 Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 270 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A3535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103429 restraints weight = 39394.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107360 restraints weight = 23466.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108279 restraints weight = 14690.253| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25142 Z= 0.114 Angle : 0.522 12.627 34089 Z= 0.254 Chirality : 0.039 0.197 3821 Planarity : 0.003 0.044 4367 Dihedral : 5.347 85.295 3377 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 1.81 % Allowed : 13.41 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.16), residues: 3035 helix: 2.40 (0.12), residues: 1781 sheet: -0.96 (0.31), residues: 263 loop : 0.54 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.003 0.001 HIS A2218 PHE 0.016 0.001 PHE A3813 TYR 0.015 0.001 TYR A2748 ARG 0.009 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1445) hydrogen bonds : angle 3.83647 ( 4197) covalent geometry : bond 0.00263 (25142) covalent geometry : angle 0.52220 (34089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0137 (tpt) cc_final: -0.2966 (mtt) REVERT: A 1398 MET cc_start: 0.6812 (tpp) cc_final: 0.6376 (ptt) REVERT: A 1488 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.5766 (mtm-85) REVERT: A 1527 LEU cc_start: 0.6864 (mt) cc_final: 0.6624 (tt) REVERT: A 1541 GLN cc_start: 0.7114 (tt0) cc_final: 0.6721 (tt0) REVERT: A 1892 MET cc_start: 0.9015 (mmp) cc_final: 0.8786 (mmp) REVERT: A 1973 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: A 2286 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7973 (tppt) REVERT: A 2320 ASP cc_start: 0.7613 (t0) cc_final: 0.7186 (p0) REVERT: A 2415 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 2505 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 2970 GLU cc_start: 0.8424 (mp0) cc_final: 0.8119 (mp0) REVERT: A 3059 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 3479 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5853 (mp) REVERT: A 3489 TRP cc_start: 0.5606 (OUTLIER) cc_final: 0.5248 (m-10) REVERT: A 3661 LEU cc_start: 0.8605 (mm) cc_final: 0.8336 (tp) REVERT: A 3771 GLU cc_start: 0.7419 (pt0) cc_final: 0.7076 (pt0) REVERT: A 3775 ARG cc_start: 0.8485 (ptp90) cc_final: 0.8161 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 3785 GLU cc_start: 0.7511 (mp0) cc_final: 0.7304 (mp0) REVERT: A 4343 MET cc_start: 0.8197 (ttp) cc_final: 0.7847 (ttp) REVERT: A 4344 LEU cc_start: 0.8939 (tp) cc_final: 0.8738 (tp) REVERT: A 4346 MET cc_start: 0.8301 (mmm) cc_final: 0.7866 (mmm) REVERT: A 4473 MET cc_start: 0.8351 (ttt) cc_final: 0.8049 (ttt) REVERT: A 4629 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7625 (ptmt) REVERT: A 4646 GLU cc_start: 0.6659 (tt0) cc_final: 0.6394 (tt0) outliers start: 49 outliers final: 35 residues processed: 310 average time/residue: 0.3795 time to fit residues: 187.4381 Evaluate side-chains 305 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2501 SER Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 159 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 179 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A3092 ASN A3535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103695 restraints weight = 39287.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107783 restraints weight = 23415.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108702 restraints weight = 14712.877| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25142 Z= 0.116 Angle : 0.526 12.484 34089 Z= 0.257 Chirality : 0.039 0.199 3821 Planarity : 0.004 0.054 4367 Dihedral : 5.295 85.911 3377 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 1.74 % Allowed : 13.67 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.16), residues: 3035 helix: 2.40 (0.12), residues: 1781 sheet: -0.95 (0.31), residues: 264 loop : 0.55 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1490 HIS 0.003 0.001 HIS A2218 PHE 0.016 0.001 PHE A3813 TYR 0.015 0.001 TYR A2748 ARG 0.015 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1445) hydrogen bonds : angle 3.82511 ( 4197) covalent geometry : bond 0.00268 (25142) covalent geometry : angle 0.52634 (34089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 MET cc_start: -0.0249 (tpt) cc_final: -0.2915 (mtt) REVERT: A 1398 MET cc_start: 0.6775 (tpp) cc_final: 0.6384 (ptt) REVERT: A 1417 MET cc_start: 0.3228 (mmp) cc_final: 0.2372 (mmt) REVERT: A 1488 ARG cc_start: 0.6629 (mtm-85) cc_final: 0.5694 (mtm-85) REVERT: A 1527 LEU cc_start: 0.6848 (mt) cc_final: 0.6616 (tt) REVERT: A 1541 GLN cc_start: 0.7083 (tt0) cc_final: 0.6709 (tt0) REVERT: A 1892 MET cc_start: 0.8976 (mmp) cc_final: 0.8767 (mmp) REVERT: A 1973 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: A 2286 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8006 (tppt) REVERT: A 2415 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 2505 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: A 2970 GLU cc_start: 0.8435 (mp0) cc_final: 0.8121 (mp0) REVERT: A 3007 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7454 (mtp85) REVERT: A 3059 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 3479 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5853 (mp) REVERT: A 3489 TRP cc_start: 0.5580 (OUTLIER) cc_final: 0.5227 (m-10) REVERT: A 3551 GLU cc_start: 0.6854 (mp0) cc_final: 0.6531 (mp0) REVERT: A 3661 LEU cc_start: 0.8592 (mm) cc_final: 0.8326 (tp) REVERT: A 3771 GLU cc_start: 0.7515 (pt0) cc_final: 0.7201 (pt0) REVERT: A 3775 ARG cc_start: 0.8478 (ptp90) cc_final: 0.8154 (ptp-110) REVERT: A 3776 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 4095 MET cc_start: 0.8286 (mmt) cc_final: 0.8081 (tpp) REVERT: A 4343 MET cc_start: 0.8158 (ttp) cc_final: 0.7804 (ttp) REVERT: A 4346 MET cc_start: 0.8230 (mmm) cc_final: 0.7797 (mmm) REVERT: A 4473 MET cc_start: 0.8363 (ttt) cc_final: 0.8046 (ttt) REVERT: A 4629 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7646 (ptmt) REVERT: A 4646 GLU cc_start: 0.6705 (tt0) cc_final: 0.6487 (tt0) outliers start: 47 outliers final: 38 residues processed: 302 average time/residue: 0.3672 time to fit residues: 177.1786 Evaluate side-chains 309 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1832 ASN Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2501 SER Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3004 PHE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4552 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 104 optimal weight: 0.5980 chunk 303 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 250 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A3535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104000 restraints weight = 38992.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107473 restraints weight = 21832.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109345 restraints weight = 14029.407| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25142 Z= 0.109 Angle : 0.521 12.576 34089 Z= 0.252 Chirality : 0.038 0.199 3821 Planarity : 0.004 0.061 4367 Dihedral : 5.228 86.991 3377 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.70 % Allowed : 13.93 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.16), residues: 3035 helix: 2.43 (0.12), residues: 1782 sheet: -0.90 (0.32), residues: 264 loop : 0.55 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1490 HIS 0.003 0.001 HIS A2218 PHE 0.015 0.001 PHE A3813 TYR 0.024 0.001 TYR A1546 ARG 0.013 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 1445) hydrogen bonds : angle 3.78724 ( 4197) covalent geometry : bond 0.00250 (25142) covalent geometry : angle 0.52142 (34089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7260.07 seconds wall clock time: 128 minutes 17.44 seconds (7697.44 seconds total)