Starting phenix.real_space_refine on Sat Jun 21 17:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.map" model { file = "/net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dha_46861/06_2025/9dha_46861.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 10 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15626 2.51 5 N 4246 2.21 5 O 4583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3038, 24471 Classifications: {'peptide': 3038} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2904} Chain breaks: 4 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {' MG': 1, 'ADP': 2, 'ANP': 1, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.88, per 1000 atoms: 0.56 Number of scatterers: 24588 At special positions: 0 Unit cell: (119.202, 170.123, 172.438, 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 10 15.00 Mg 1 11.99 O 4583 8.00 N 4246 7.00 C 15626 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: 6.55 Conformation dependent library (CDL) restraints added in 3.3 seconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 63.9% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1349 removed outlier: 3.730A pdb=" N GLN A1349 " --> pdb=" O GLN A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1375 through 1379 removed outlier: 3.552A pdb=" N GLN A1379 " --> pdb=" O ARG A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1404 removed outlier: 4.360A pdb=" N MET A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A1399 " --> pdb=" O LYS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.621A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1473 removed outlier: 3.519A pdb=" N VAL A1446 " --> pdb=" O ASN A1442 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.507A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 3.682A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.572A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1594 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 1651 removed outlier: 3.638A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1657 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 4.075A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.648A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1773 removed outlier: 4.136A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.556A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.686A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1829 " --> pdb=" O LEU A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1841 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 1939 through 1952 removed outlier: 4.592A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1985 removed outlier: 3.566A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.618A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) 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: 3.940A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 3.852A pdb=" N ASN A2130 " --> pdb=" O GLU A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.632A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2153 through 2165 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 2255 through 2259 removed outlier: 3.507A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2266 removed outlier: 3.647A pdb=" N TYR A2265 " --> pdb=" O LYS A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2359 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2395 through 2400 Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.722A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.950A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.578A 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 2587 removed outlier: 4.026A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.797A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.221A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 removed outlier: 3.505A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.545A pdb=" N THR A2770 " --> pdb=" O ALA A2766 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.932A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.535A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2885 through 2903 removed outlier: 3.813A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A2903 " --> pdb=" O VAL A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.793A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3082 through 3089 removed outlier: 3.608A pdb=" N PHE A3086 " --> pdb=" O SER A3082 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A3089 " --> pdb=" O LEU A3085 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.577A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.774A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 removed outlier: 3.547A pdb=" N ARG A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 3.672A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 3.721A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.633A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 6.066A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 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 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.845A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 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 4014 Processing helix chain 'A' and resid 4017 through 4023 removed outlier: 4.232A pdb=" N ILE A4020 " --> pdb=" O PHE A4017 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.804A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.806A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.662A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) 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 4116 removed outlier: 3.920A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.676A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.580A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4192 removed outlier: 4.121A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4193 through 4197 Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.752A 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: 3.616A 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 4287 through 4291 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 4346 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 3.831A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4506 removed outlier: 7.718A pdb=" N ALA A4501 " --> pdb=" O ALA A4497 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS A4502 " --> pdb=" O SER A4498 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A4503 " --> pdb=" O GLY A4499 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.753A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 10.511A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.291A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) 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 2254 removed outlier: 6.405A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2267 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.228A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.705A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.189A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.095A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.022A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 3.894A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.229A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4563 through 4571 removed outlier: 4.501A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1456 hydrogen bonds defined for protein. 4224 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: 15.44 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7000 1.33 - 1.45: 4042 1.45 - 1.57: 13848 1.57 - 1.69: 17 1.69 - 1.81: 206 Bond restraints: 25113 Sorted by residual: bond pdb=" O3A ANP A4703 " pdb=" PB ANP A4703 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O5' ANP A4703 " pdb=" PA ANP A4703 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3G ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 1.528 1.580 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" O2B ANP A4703 " pdb=" PB ANP A4703 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.73e+00 ... (remaining 25108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 33914 3.55 - 7.11: 123 7.11 - 10.66: 13 10.66 - 14.22: 1 14.22 - 17.77: 1 Bond angle restraints: 34052 Sorted by residual: angle pdb=" PB ANP A4703 " pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 126.95 109.18 17.77 3.00e+00 1.11e-01 3.51e+01 angle pdb=" CB ARG A3206 " pdb=" CG ARG A3206 " pdb=" CD ARG A3206 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" O1B ANP A4703 " pdb=" PB ANP A4703 " pdb=" O2B ANP A4703 " ideal model delta sigma weight residual 120.08 109.39 10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA ARG A1388 " pdb=" CB ARG A1388 " pdb=" CG ARG A1388 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.11e+01 angle pdb=" N GLN A3792 " pdb=" CA GLN A3792 " pdb=" CB GLN A3792 " ideal model delta sigma weight residual 110.28 115.45 -5.17 1.55e+00 4.16e-01 1.11e+01 ... (remaining 34047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13728 17.98 - 35.95: 1227 35.95 - 53.93: 190 53.93 - 71.90: 65 71.90 - 89.88: 47 Dihedral angle restraints: 15257 sinusoidal: 6361 harmonic: 8896 Sorted by residual: dihedral pdb=" CA LYS A2349 " pdb=" C LYS A2349 " pdb=" N TYR A2350 " pdb=" CA TYR A2350 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 -149.33 89.33 1 2.00e+01 2.50e-03 2.37e+01 dihedral pdb=" CA THR A4628 " pdb=" C THR A4628 " pdb=" N LYS A4629 " pdb=" CA LYS A4629 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 15254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3206 0.055 - 0.109: 561 0.109 - 0.164: 47 0.164 - 0.219: 1 0.219 - 0.273: 1 Chirality restraints: 3816 Sorted by residual: chirality pdb=" C3' ANP A4703 " pdb=" C2' ANP A4703 " pdb=" C4' ANP A4703 " pdb=" O3' ANP A4703 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU A3753 " pdb=" CB LEU A3753 " pdb=" CD1 LEU A3753 " pdb=" CD2 LEU A3753 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB THR A3685 " pdb=" CA THR A3685 " pdb=" OG1 THR A3685 " pdb=" CG2 THR A3685 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 3813 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1388 " 0.172 9.50e-02 1.11e+02 7.76e-02 4.63e+00 pdb=" NE ARG A1388 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A1388 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A1388 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A1388 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A2524 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A2525 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A2525 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2525 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A2731 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A2732 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A2732 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A2732 " 0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 256 2.57 - 3.15: 20918 3.15 - 3.73: 40959 3.73 - 4.32: 53455 4.32 - 4.90: 88391 Nonbonded interactions: 203979 Sorted by model distance: nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4705 " model vdw 1.985 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4705 " model vdw 2.113 2.170 nonbonded pdb=" O PRO A1511 " pdb=" NZ LYS A1514 " model vdw 2.114 3.120 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.193 3.040 nonbonded pdb=" NH1 ARG A3167 " pdb=" O THR A3168 " model vdw 2.196 3.120 ... (remaining 203974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.340 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: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 62.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 25113 Z= 0.144 Angle : 0.624 17.771 34052 Z= 0.319 Chirality : 0.040 0.273 3816 Planarity : 0.004 0.078 4362 Dihedral : 14.917 89.877 9477 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.17 (0.16), residues: 3028 helix: 1.59 (0.13), residues: 1730 sheet: -0.50 (0.33), residues: 239 loop : -0.18 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3489 HIS 0.007 0.001 HIS A2730 PHE 0.028 0.001 PHE A2682 TYR 0.017 0.001 TYR A1393 ARG 0.017 0.001 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.12980 ( 1456) hydrogen bonds : angle 5.79652 ( 4224) covalent geometry : bond 0.00294 (25113) covalent geometry : angle 0.62383 (34052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1457 MET cc_start: 0.8976 (ttt) cc_final: 0.8557 (mtp) REVERT: A 1531 MET cc_start: 0.8765 (tpt) cc_final: 0.8534 (tpt) REVERT: A 2953 MET cc_start: 0.7708 (ttm) cc_final: 0.7392 (mtp) REVERT: A 3205 LEU cc_start: 0.9076 (mt) cc_final: 0.8150 (mt) REVERT: A 3776 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 4063 ASN cc_start: 0.8850 (m-40) cc_final: 0.8641 (m-40) REVERT: A 4190 ILE cc_start: 0.9065 (pt) cc_final: 0.8790 (mt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3740 time to fit residues: 140.1547 Evaluate side-chains 171 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 237 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1495 ASN ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2057 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059614 restraints weight = 88494.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061309 restraints weight = 42549.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062406 restraints weight = 26926.083| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25113 Z= 0.131 Angle : 0.551 8.730 34052 Z= 0.280 Chirality : 0.040 0.172 3816 Planarity : 0.004 0.050 4362 Dihedral : 6.580 98.763 3391 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.55 % Allowed : 5.88 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 3028 helix: 1.76 (0.12), residues: 1770 sheet: -0.56 (0.32), residues: 252 loop : -0.14 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.010 0.001 HIS A4389 PHE 0.038 0.001 PHE A3698 TYR 0.020 0.001 TYR A3812 ARG 0.008 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1456) hydrogen bonds : angle 4.52351 ( 4224) covalent geometry : bond 0.00289 (25113) covalent geometry : angle 0.55135 (34052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1814 GLU cc_start: 0.8398 (tp30) cc_final: 0.8157 (tp30) REVERT: A 3169 MET cc_start: 0.7315 (mtp) cc_final: 0.7020 (mtp) REVERT: A 3206 ARG cc_start: 0.8038 (mmp-170) cc_final: 0.7780 (ptm160) REVERT: A 3776 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 3788 ASP cc_start: 0.7886 (t0) cc_final: 0.7612 (t0) REVERT: A 4063 ASN cc_start: 0.8906 (m-40) cc_final: 0.8668 (m-40) REVERT: A 4192 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 4344 LEU cc_start: 0.9182 (tp) cc_final: 0.8893 (tp) outliers start: 15 outliers final: 7 residues processed: 217 average time/residue: 0.3727 time to fit residues: 131.9699 Evaluate side-chains 168 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 162 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1495 ASN ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2860 ASN A4012 ASN ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4291 HIS A4595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058610 restraints weight = 88237.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060311 restraints weight = 42471.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061407 restraints weight = 26790.873| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25113 Z= 0.163 Angle : 0.546 10.091 34052 Z= 0.275 Chirality : 0.039 0.147 3816 Planarity : 0.004 0.051 4362 Dihedral : 6.497 101.066 3391 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.89 % Allowed : 8.88 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.16), residues: 3028 helix: 1.84 (0.12), residues: 1775 sheet: -0.60 (0.32), residues: 252 loop : -0.13 (0.21), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.004 0.001 HIS A2918 PHE 0.025 0.001 PHE A3698 TYR 0.017 0.001 TYR A3812 ARG 0.005 0.000 ARG A4462 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1456) hydrogen bonds : angle 4.37622 ( 4224) covalent geometry : bond 0.00366 (25113) covalent geometry : angle 0.54562 (34052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1457 MET cc_start: 0.8775 (ttt) cc_final: 0.8567 (mtp) REVERT: A 3169 MET cc_start: 0.7129 (mtp) cc_final: 0.6924 (mtp) REVERT: A 3776 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 3788 ASP cc_start: 0.8009 (t0) cc_final: 0.7737 (t0) REVERT: A 4063 ASN cc_start: 0.8930 (m-40) cc_final: 0.8688 (m-40) REVERT: A 4192 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 4344 LEU cc_start: 0.9213 (tp) cc_final: 0.8895 (tp) outliers start: 24 outliers final: 16 residues processed: 189 average time/residue: 0.3603 time to fit residues: 113.1595 Evaluate side-chains 170 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 117 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 268 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057587 restraints weight = 89801.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059211 restraints weight = 44449.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060274 restraints weight = 28513.344| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25113 Z= 0.196 Angle : 0.563 9.525 34052 Z= 0.284 Chirality : 0.040 0.165 3816 Planarity : 0.004 0.052 4362 Dihedral : 6.416 98.486 3391 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.15 % Allowed : 11.21 % Favored : 87.64 % 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: 1.47 (0.16), residues: 3028 helix: 1.88 (0.12), residues: 1776 sheet: -0.74 (0.32), residues: 258 loop : -0.10 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.009 0.001 HIS A2918 PHE 0.024 0.002 PHE A4410 TYR 0.018 0.001 TYR A3026 ARG 0.006 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 1456) hydrogen bonds : angle 4.34896 ( 4224) covalent geometry : bond 0.00442 (25113) covalent geometry : angle 0.56306 (34052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1402 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 1417 MET cc_start: 0.6908 (ptp) cc_final: 0.6505 (ptp) REVERT: A 1457 MET cc_start: 0.8816 (ttt) cc_final: 0.8554 (mtp) REVERT: A 3030 MET cc_start: 0.7218 (mmt) cc_final: 0.6819 (mmt) REVERT: A 3776 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 4021 MET cc_start: 0.9098 (mmp) cc_final: 0.8855 (mmm) REVERT: A 4344 LEU cc_start: 0.9174 (tp) cc_final: 0.8826 (tp) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.3769 time to fit residues: 118.5773 Evaluate side-chains 179 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 299 optimal weight: 0.4980 chunk 281 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3009 ASN A3595 GLN A3735 GLN A4347 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058476 restraints weight = 88957.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060123 restraints weight = 44007.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.061209 restraints weight = 28276.749| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25113 Z= 0.129 Angle : 0.524 10.804 34052 Z= 0.262 Chirality : 0.039 0.245 3816 Planarity : 0.004 0.050 4362 Dihedral : 6.242 94.310 3391 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.22 % Allowed : 12.13 % Favored : 86.64 % 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: 1.61 (0.16), residues: 3028 helix: 1.99 (0.12), residues: 1769 sheet: -0.69 (0.32), residues: 257 loop : -0.04 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 PHE 0.029 0.001 PHE A4410 TYR 0.017 0.001 TYR A3812 ARG 0.005 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1456) hydrogen bonds : angle 4.21438 ( 4224) covalent geometry : bond 0.00287 (25113) covalent geometry : angle 0.52406 (34052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1402 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 1417 MET cc_start: 0.6735 (ptp) cc_final: 0.6213 (ptp) REVERT: A 1457 MET cc_start: 0.8820 (ttt) cc_final: 0.8402 (ttt) REVERT: A 1461 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: A 1769 MET cc_start: 0.8769 (mmm) cc_final: 0.8556 (mmm) REVERT: A 2423 MET cc_start: 0.8269 (mtp) cc_final: 0.8003 (mtm) REVERT: A 2755 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8264 (tpp) REVERT: A 3030 MET cc_start: 0.7112 (mmt) cc_final: 0.6583 (mmt) REVERT: A 3776 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 4021 MET cc_start: 0.9121 (mmp) cc_final: 0.8890 (mmm) REVERT: A 4344 LEU cc_start: 0.9154 (tp) cc_final: 0.8829 (tp) outliers start: 33 outliers final: 20 residues processed: 204 average time/residue: 0.3620 time to fit residues: 122.5786 Evaluate side-chains 179 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 226 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 188 optimal weight: 0.9990 chunk 265 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2698 GLN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059339 restraints weight = 88292.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061060 restraints weight = 42560.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062173 restraints weight = 26787.722| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25113 Z= 0.106 Angle : 0.513 10.307 34052 Z= 0.255 Chirality : 0.038 0.213 3816 Planarity : 0.004 0.076 4362 Dihedral : 6.005 91.448 3391 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.07 % Allowed : 12.73 % Favored : 86.20 % 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: 1.68 (0.16), residues: 3028 helix: 2.06 (0.12), residues: 1776 sheet: -0.73 (0.32), residues: 264 loop : -0.02 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2918 PHE 0.017 0.001 PHE A1836 TYR 0.017 0.001 TYR A1480 ARG 0.008 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1456) hydrogen bonds : angle 4.12221 ( 4224) covalent geometry : bond 0.00229 (25113) covalent geometry : angle 0.51331 (34052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2222 MET cc_start: 0.8929 (mtm) cc_final: 0.8653 (mtm) REVERT: A 2423 MET cc_start: 0.8356 (mtp) cc_final: 0.8088 (mtm) REVERT: A 2755 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: A 2799 MET cc_start: 0.9058 (mmm) cc_final: 0.8771 (mmm) REVERT: A 3030 MET cc_start: 0.7205 (mmt) cc_final: 0.6596 (mmt) REVERT: A 3776 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 4344 LEU cc_start: 0.9170 (tp) cc_final: 0.8859 (tp) outliers start: 29 outliers final: 19 residues processed: 201 average time/residue: 0.3463 time to fit residues: 115.8220 Evaluate side-chains 179 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 232 optimal weight: 0.9990 chunk 122 optimal weight: 0.0170 chunk 22 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3202 ASN ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057490 restraints weight = 90100.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059100 restraints weight = 45216.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060142 restraints weight = 29315.220| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25113 Z= 0.189 Angle : 0.556 10.940 34052 Z= 0.280 Chirality : 0.040 0.183 3816 Planarity : 0.004 0.076 4362 Dihedral : 5.978 90.954 3391 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.37 % Allowed : 12.91 % Favored : 85.72 % 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: 1.65 (0.16), residues: 3028 helix: 2.03 (0.12), residues: 1772 sheet: -0.64 (0.32), residues: 257 loop : -0.05 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.005 0.001 HIS A2918 PHE 0.024 0.001 PHE A1836 TYR 0.017 0.001 TYR A2496 ARG 0.020 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1456) hydrogen bonds : angle 4.24040 ( 4224) covalent geometry : bond 0.00425 (25113) covalent geometry : angle 0.55633 (34052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8303 (mm-30) REVERT: A 1488 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: A 1769 MET cc_start: 0.8683 (mmm) cc_final: 0.8462 (mmm) REVERT: A 2655 LEU cc_start: 0.8422 (mp) cc_final: 0.7908 (tt) REVERT: A 2755 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8260 (tpp) REVERT: A 2799 MET cc_start: 0.9145 (mmm) cc_final: 0.8824 (mmm) REVERT: A 3030 MET cc_start: 0.7175 (mmt) cc_final: 0.6600 (mmt) REVERT: A 3601 MET cc_start: 0.9048 (mmt) cc_final: 0.8629 (mmt) REVERT: A 3776 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 4344 LEU cc_start: 0.9224 (tp) cc_final: 0.8900 (tp) outliers start: 37 outliers final: 25 residues processed: 189 average time/residue: 0.3888 time to fit residues: 125.1072 Evaluate side-chains 181 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 68 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058791 restraints weight = 88992.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060441 restraints weight = 44631.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061517 restraints weight = 28764.659| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25113 Z= 0.116 Angle : 0.529 11.095 34052 Z= 0.263 Chirality : 0.039 0.182 3816 Planarity : 0.004 0.129 4362 Dihedral : 5.873 88.780 3391 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.18 % Allowed : 13.69 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 3028 helix: 2.09 (0.12), residues: 1768 sheet: -0.65 (0.32), residues: 258 loop : -0.02 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2918 PHE 0.028 0.001 PHE A3957 TYR 0.016 0.001 TYR A3812 ARG 0.027 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1456) hydrogen bonds : angle 4.14596 ( 4224) covalent geometry : bond 0.00256 (25113) covalent geometry : angle 0.52883 (34052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: A 1769 MET cc_start: 0.8692 (mmm) cc_final: 0.8489 (mmm) REVERT: A 2222 MET cc_start: 0.8973 (mtm) cc_final: 0.8683 (mtm) REVERT: A 2423 MET cc_start: 0.8294 (mtp) cc_final: 0.7984 (mtm) REVERT: A 2755 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8236 (tpp) REVERT: A 2799 MET cc_start: 0.9135 (mmm) cc_final: 0.8832 (mmm) REVERT: A 3030 MET cc_start: 0.7052 (mmt) cc_final: 0.6435 (mmt) REVERT: A 3199 MET cc_start: 0.8803 (ppp) cc_final: 0.8512 (ppp) REVERT: A 3601 MET cc_start: 0.9036 (mmt) cc_final: 0.8615 (mmt) REVERT: A 3776 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 4344 LEU cc_start: 0.9186 (tp) cc_final: 0.8875 (tp) outliers start: 32 outliers final: 24 residues processed: 192 average time/residue: 0.3700 time to fit residues: 117.7722 Evaluate side-chains 185 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058603 restraints weight = 89355.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.060306 restraints weight = 42978.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061404 restraints weight = 27075.552| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25113 Z= 0.128 Angle : 0.533 11.908 34052 Z= 0.264 Chirality : 0.039 0.313 3816 Planarity : 0.004 0.096 4362 Dihedral : 5.801 88.165 3391 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.22 % Allowed : 13.87 % Favored : 84.91 % 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: 1.75 (0.16), residues: 3028 helix: 2.11 (0.12), residues: 1768 sheet: -0.61 (0.32), residues: 252 loop : -0.01 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.005 0.001 HIS A2918 PHE 0.022 0.001 PHE A3957 TYR 0.015 0.001 TYR A3812 ARG 0.021 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1456) hydrogen bonds : angle 4.14255 ( 4224) covalent geometry : bond 0.00287 (25113) covalent geometry : angle 0.53309 (34052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: A 1769 MET cc_start: 0.8661 (mmm) cc_final: 0.8460 (mmm) REVERT: A 2222 MET cc_start: 0.8990 (mtm) cc_final: 0.8720 (mtm) REVERT: A 2423 MET cc_start: 0.8405 (mtp) cc_final: 0.8099 (mtm) REVERT: A 2510 MET cc_start: 0.8355 (tpp) cc_final: 0.8148 (tpt) REVERT: A 2578 GLU cc_start: 0.8544 (tt0) cc_final: 0.8269 (mt-10) REVERT: A 2755 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8224 (tpp) REVERT: A 2799 MET cc_start: 0.9151 (mmm) cc_final: 0.8772 (mmm) REVERT: A 3030 MET cc_start: 0.7024 (mmt) cc_final: 0.6389 (mmt) REVERT: A 3199 MET cc_start: 0.8798 (ppp) cc_final: 0.8534 (ppp) REVERT: A 3601 MET cc_start: 0.9025 (mmt) cc_final: 0.8614 (mmt) REVERT: A 3776 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 4007 MET cc_start: 0.8285 (ttp) cc_final: 0.8062 (ttp) REVERT: A 4344 LEU cc_start: 0.9217 (tp) cc_final: 0.8906 (tp) outliers start: 33 outliers final: 26 residues processed: 185 average time/residue: 0.3615 time to fit residues: 112.5241 Evaluate side-chains 184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058075 restraints weight = 89693.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059686 restraints weight = 44734.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060734 restraints weight = 28885.083| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25113 Z= 0.157 Angle : 0.559 11.994 34052 Z= 0.278 Chirality : 0.040 0.246 3816 Planarity : 0.004 0.080 4362 Dihedral : 5.775 87.541 3391 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.07 % Allowed : 14.17 % Favored : 84.76 % 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: 1.72 (0.16), residues: 3028 helix: 2.09 (0.12), residues: 1769 sheet: -0.53 (0.33), residues: 250 loop : -0.05 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4105 HIS 0.005 0.001 HIS A2918 PHE 0.022 0.001 PHE A1836 TYR 0.015 0.001 TYR A3812 ARG 0.015 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1456) hydrogen bonds : angle 4.20071 ( 4224) covalent geometry : bond 0.00356 (25113) covalent geometry : angle 0.55878 (34052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8288 (mm-30) REVERT: A 1769 MET cc_start: 0.8650 (mmm) cc_final: 0.8449 (mmm) REVERT: A 1934 GLU cc_start: 0.7727 (pm20) cc_final: 0.7391 (pm20) REVERT: A 2423 MET cc_start: 0.8375 (mtp) cc_final: 0.8078 (mtm) REVERT: A 2578 GLU cc_start: 0.8509 (tt0) cc_final: 0.8250 (mt-10) REVERT: A 2755 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8570 (ttm) REVERT: A 2799 MET cc_start: 0.9162 (mmm) cc_final: 0.8786 (mmm) REVERT: A 3030 MET cc_start: 0.7021 (mmt) cc_final: 0.6392 (mmt) REVERT: A 3199 MET cc_start: 0.8791 (ppp) cc_final: 0.8527 (ppp) REVERT: A 3579 MET cc_start: 0.8957 (mmt) cc_final: 0.8395 (mmt) REVERT: A 3601 MET cc_start: 0.8941 (mmt) cc_final: 0.8538 (mmt) REVERT: A 3776 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 4007 MET cc_start: 0.8244 (ttp) cc_final: 0.8036 (ttp) REVERT: A 4344 LEU cc_start: 0.9226 (tp) cc_final: 0.8916 (tp) outliers start: 29 outliers final: 25 residues processed: 181 average time/residue: 0.3617 time to fit residues: 109.7945 Evaluate side-chains 181 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 ASP Chi-restraints excluded: chain A residue 1461 GLU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2536 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058479 restraints weight = 88976.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060167 restraints weight = 42908.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061272 restraints weight = 27073.273| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25113 Z= 0.133 Angle : 0.545 12.123 34052 Z= 0.270 Chirality : 0.039 0.212 3816 Planarity : 0.004 0.071 4362 Dihedral : 5.710 87.873 3391 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.15 % Allowed : 14.21 % Favored : 84.65 % 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: 1.75 (0.16), residues: 3028 helix: 2.11 (0.12), residues: 1768 sheet: -0.55 (0.32), residues: 253 loop : -0.01 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2918 PHE 0.020 0.001 PHE A1836 TYR 0.015 0.001 TYR A3812 ARG 0.014 0.000 ARG A1388 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 1456) hydrogen bonds : angle 4.16007 ( 4224) covalent geometry : bond 0.00299 (25113) covalent geometry : angle 0.54506 (34052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7769.65 seconds wall clock time: 135 minutes 52.54 seconds (8152.54 seconds total)