Starting phenix.real_space_refine on Fri Feb 6 13:49:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.map" model { file = "/net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgp_46843/02_2026/9dgp_46843.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.046 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 11 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 15622 2.51 5 N 4249 2.21 5 O 4580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24585 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3037, 24453 Classifications: {'peptide': 3037} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 132, 'TRANS': 2901} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 3037, 24453 Classifications: {'peptide': 3037} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 132, 'TRANS': 2901} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 24962 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 124 Unusual residues: {' MG': 4, 'ADP': 1, 'ANP': 2, 'ATP': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 9.29, per 1000 atoms: 0.38 Number of scatterers: 24585 At special positions: 0 Unit cell: (119.784, 161.448, 182.28, 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 119 16.00 P 11 15.00 Mg 4 11.99 O 4580 8.00 N 4249 7.00 C 15622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 63.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1355 through 1373 removed outlier: 3.505A pdb=" N PHE A1373 " --> pdb=" O GLN A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1420 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.650A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1473 Processing helix chain 'A' and resid 1489 through 1508 Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 4.302A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 3.895A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.734A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 4.166A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1773 Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.582A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1824 removed outlier: 3.519A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1829 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1985 removed outlier: 3.580A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2034 No H-bonds generated for 'chain 'A' and resid 2032 through 2034' Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.051A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2295 No H-bonds generated for 'chain 'A' and resid 2293 through 2295' 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 2394 through 2400 removed outlier: 4.032A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2431 through 2443 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.603A 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: 3.839A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.120A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.048A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.741A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.608A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2903 removed outlier: 3.565A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (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 2996 through 3000 Processing helix chain 'A' and resid 3001 through 3014 removed outlier: 3.560A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3082 through 3089 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.703A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3517 removed outlier: 4.748A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 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: 3.789A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.071A 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 3873 removed outlier: 3.586A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.160A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.513A 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 3970 removed outlier: 4.065A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.880A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 4.037A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 4.126A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4116 removed outlier: 3.624A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4174 through 4195 removed outlier: 4.474A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 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 4325 through 4346 removed outlier: 4.494A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4407 removed outlier: 3.812A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A4407 " --> pdb=" O ASP A4403 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4440 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 Processing helix chain 'A' and resid 4502 through 4507 removed outlier: 3.604A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) 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 removed outlier: 3.585A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.113A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.773A 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: 7.762A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.613A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.200A 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 2248 through 2251 removed outlier: 6.620A pdb=" N GLU A2248 " --> pdb=" O ARG A2298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TRP A2300 " --> pdb=" O GLU A2248 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ARG A2340 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 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: 6.532A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.750A 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 removed outlier: 3.907A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.364A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.719A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3661 through 3664 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.326A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 3.703A 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 Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.776A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1460 hydrogen bonds defined for protein. 4251 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: 7.97 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8099 1.34 - 1.46: 4624 1.46 - 1.58: 12169 1.58 - 1.70: 13 1.70 - 1.81: 203 Bond restraints: 25108 Sorted by residual: bond pdb=" N ILE A2861 " pdb=" CA ILE A2861 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N VAL A4545 " pdb=" CA VAL A4545 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.10e-02 8.26e+03 1.04e+01 bond pdb=" N VAL A4605 " pdb=" CA VAL A4605 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" N ILE A4626 " pdb=" CA ILE A4626 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.71e+00 bond pdb=" N ILE A3959 " pdb=" CA ILE A3959 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.95e+00 ... (remaining 25103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 33164 2.25 - 4.49: 841 4.49 - 6.74: 42 6.74 - 8.98: 2 8.98 - 11.23: 1 Bond angle restraints: 34050 Sorted by residual: angle pdb=" C LYS A1409 " pdb=" CA LYS A1409 " pdb=" CB LYS A1409 " ideal model delta sigma weight residual 115.79 109.96 5.83 1.19e+00 7.06e-01 2.40e+01 angle pdb=" N LEU A1416 " pdb=" CA LEU A1416 " pdb=" C LEU A1416 " ideal model delta sigma weight residual 111.07 106.59 4.48 1.07e+00 8.73e-01 1.76e+01 angle pdb=" C GLU A2904 " pdb=" CA GLU A2904 " pdb=" CB GLU A2904 " ideal model delta sigma weight residual 116.34 110.62 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" CA THR A2428 " pdb=" C THR A2428 " pdb=" O THR A2428 " ideal model delta sigma weight residual 121.08 117.78 3.30 8.90e-01 1.26e+00 1.38e+01 angle pdb=" N GLY A1773 " pdb=" CA GLY A1773 " pdb=" C GLY A1773 " ideal model delta sigma weight residual 115.43 110.38 5.05 1.41e+00 5.03e-01 1.28e+01 ... (remaining 34045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 14680 28.56 - 57.12: 482 57.12 - 85.68: 113 85.68 - 114.24: 7 114.24 - 142.80: 1 Dihedral angle restraints: 15283 sinusoidal: 6383 harmonic: 8900 Sorted by residual: dihedral pdb=" O1A ANP A4703 " pdb=" O3A ANP A4703 " pdb=" PA ANP A4703 " pdb=" PB ANP A4703 " ideal model delta sinusoidal sigma weight residual 83.11 -59.69 142.80 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA CYS A2712 " pdb=" C CYS A2712 " pdb=" N ASN A2713 " pdb=" CA ASN A2713 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" O1A ANP A4704 " pdb=" O3A ANP A4704 " pdb=" PA ANP A4704 " pdb=" PB ANP A4704 " ideal model delta sinusoidal sigma weight residual 83.11 -26.27 109.38 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 15280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2778 0.045 - 0.091: 697 0.091 - 0.136: 270 0.136 - 0.182: 50 0.182 - 0.227: 23 Chirality restraints: 3818 Sorted by residual: chirality pdb=" CA ILE A4544 " pdb=" N ILE A4544 " pdb=" C ILE A4544 " pdb=" CB ILE A4544 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE A3914 " pdb=" N ILE A3914 " pdb=" C ILE A3914 " pdb=" CB ILE A3914 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A1665 " pdb=" N ILE A1665 " pdb=" C ILE A1665 " pdb=" CB ILE A1665 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3815 not shown) Planarity restraints: 4361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4302 " 0.383 9.50e-02 1.11e+02 1.72e-01 1.81e+01 pdb=" NE ARG A4302 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A4302 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A4302 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A4302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2292 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.64e+01 pdb=" NE ARG A2292 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A2292 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A2292 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A2292 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1360 " 0.345 9.50e-02 1.11e+02 1.55e-01 1.48e+01 pdb=" NE ARG A1360 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A1360 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A1360 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1360 " 0.011 2.00e-02 2.50e+03 ... (remaining 4358 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 156 2.54 - 3.13: 19659 3.13 - 3.72: 39860 3.72 - 4.31: 56285 4.31 - 4.90: 94201 Nonbonded interactions: 210161 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.948 2.170 nonbonded pdb=" OG1 THR A2602 " pdb="MG MG A4707 " model vdw 1.966 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 1.978 2.170 nonbonded pdb=" O3G ANP A4703 " pdb="MG MG A4707 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR A2944 " pdb="MG MG A4708 " model vdw 2.062 2.170 ... (remaining 210156 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=0.43 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 32.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.005 0.048 25108 Z= 0.373 Angle : 0.707 11.227 34050 Z= 0.483 Chirality : 0.050 0.227 3818 Planarity : 0.008 0.172 4361 Dihedral : 14.504 142.797 9497 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.75 % Favored : 98.08 % Rotamer: Outliers : 0.11 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3026 helix: 1.15 (0.12), residues: 1752 sheet: -0.85 (0.32), residues: 236 loop : 0.20 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1599 TYR 0.023 0.001 TYR A3836 PHE 0.024 0.002 PHE A3813 TRP 0.022 0.001 TRP A4376 HIS 0.005 0.001 HIS A1695 Details of bonding type rmsd covalent geometry : bond 0.00549 (25108) covalent geometry : angle 0.70693 (34050) hydrogen bonds : bond 0.12369 ( 1460) hydrogen bonds : angle 5.83466 ( 4251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 702 time to evaluate : 0.852 Fit side-chains REVERT: A 1346 MET cc_start: 0.6854 (tpp) cc_final: 0.6614 (tpp) REVERT: A 1395 LYS cc_start: 0.8058 (tttt) cc_final: 0.7732 (pttt) REVERT: A 1480 TYR cc_start: 0.8186 (t80) cc_final: 0.7368 (t80) REVERT: A 1842 MET cc_start: 0.9046 (ttm) cc_final: 0.8755 (ttm) REVERT: A 1876 GLN cc_start: 0.8004 (tp40) cc_final: 0.7293 (pm20) REVERT: A 1879 LEU cc_start: 0.8054 (mp) cc_final: 0.7827 (mt) REVERT: A 2446 ILE cc_start: 0.8967 (tp) cc_final: 0.8674 (tp) REVERT: A 2658 TRP cc_start: 0.7926 (m100) cc_final: 0.7531 (m100) REVERT: A 2763 ARG cc_start: 0.6931 (ptp-110) cc_final: 0.6666 (mtm180) REVERT: A 2835 ASP cc_start: 0.7566 (m-30) cc_final: 0.7264 (m-30) REVERT: A 2974 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7325 (tt0) REVERT: A 2987 ASN cc_start: 0.8303 (t0) cc_final: 0.8039 (p0) REVERT: A 2994 MET cc_start: 0.8107 (mtp) cc_final: 0.7694 (mtm) REVERT: A 3008 MET cc_start: 0.8845 (tpt) cc_final: 0.8192 (tpp) REVERT: A 3066 PHE cc_start: 0.9052 (m-80) cc_final: 0.8826 (m-80) REVERT: A 3096 ASP cc_start: 0.7933 (t70) cc_final: 0.7703 (t0) REVERT: A 3635 VAL cc_start: 0.8539 (t) cc_final: 0.8236 (t) REVERT: A 3637 ASP cc_start: 0.8085 (m-30) cc_final: 0.7697 (m-30) REVERT: A 3666 ASP cc_start: 0.7424 (p0) cc_final: 0.6468 (t0) REVERT: A 3740 LEU cc_start: 0.8296 (tp) cc_final: 0.8050 (tt) REVERT: A 4377 MET cc_start: 0.7861 (ttm) cc_final: 0.7452 (ttp) REVERT: A 4441 LYS cc_start: 0.6684 (pttm) cc_final: 0.6195 (ttpp) REVERT: A 4530 GLN cc_start: 0.7320 (tt0) cc_final: 0.6977 (mt0) REVERT: A 4573 ASN cc_start: 0.8663 (t0) cc_final: 0.8196 (t0) REVERT: A 4611 LEU cc_start: 0.8496 (tp) cc_final: 0.8294 (tt) outliers start: 2 outliers final: 0 residues processed: 703 average time/residue: 0.2003 time to fit residues: 210.4559 Evaluate side-chains 336 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A1850 GLN A1990 HIS A2003 ASN A2187 GLN A2212 GLN A2439 HIS A2476 HIS A2621 ASN A2752 ASN A2827 HIS A3175 HIS A3535 HIS A3754 ASN A3820 GLN A3838 ASN A3931 GLN A4393 GLN A4490 GLN A4508 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130771 restraints weight = 42878.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132291 restraints weight = 28637.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134307 restraints weight = 22781.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134598 restraints weight = 16274.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134869 restraints weight = 15594.298| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25108 Z= 0.209 Angle : 0.661 11.123 34050 Z= 0.336 Chirality : 0.044 0.257 3818 Planarity : 0.005 0.079 4361 Dihedral : 7.687 137.648 3410 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.02 % Rotamer: Outliers : 1.89 % Allowed : 8.62 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 3026 helix: 1.80 (0.12), residues: 1772 sheet: -0.89 (0.31), residues: 259 loop : 0.42 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A2844 TYR 0.018 0.002 TYR A2892 PHE 0.024 0.002 PHE A3996 TRP 0.019 0.002 TRP A2234 HIS 0.007 0.001 HIS A2857 Details of bonding type rmsd covalent geometry : bond 0.00493 (25108) covalent geometry : angle 0.66069 (34050) hydrogen bonds : bond 0.04695 ( 1460) hydrogen bonds : angle 4.39025 ( 4251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1457 MET cc_start: 0.6405 (tpt) cc_final: 0.6178 (tpt) REVERT: A 1837 GLU cc_start: 0.6502 (mp0) cc_final: 0.6179 (mp0) REVERT: A 1876 GLN cc_start: 0.8056 (tp40) cc_final: 0.7520 (pm20) REVERT: A 2269 ASP cc_start: 0.7178 (t0) cc_final: 0.6953 (t70) REVERT: A 2461 MET cc_start: 0.8369 (mtp) cc_final: 0.8034 (mtp) REVERT: A 2462 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 2587 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 2629 GLU cc_start: 0.7146 (mp0) cc_final: 0.6779 (mp0) REVERT: A 2658 TRP cc_start: 0.8197 (m100) cc_final: 0.7624 (m100) REVERT: A 2763 ARG cc_start: 0.6874 (ptp-110) cc_final: 0.6656 (mtm180) REVERT: A 2835 ASP cc_start: 0.7644 (m-30) cc_final: 0.7217 (m-30) REVERT: A 2987 ASN cc_start: 0.8327 (t0) cc_final: 0.7983 (p0) REVERT: A 3038 GLN cc_start: 0.7982 (mm110) cc_final: 0.7257 (mm-40) REVERT: A 3169 MET cc_start: 0.8228 (mmt) cc_final: 0.7841 (mmm) REVERT: A 3193 GLU cc_start: 0.7137 (tp30) cc_final: 0.6418 (tp30) REVERT: A 3625 SER cc_start: 0.8732 (p) cc_final: 0.8459 (m) REVERT: A 3666 ASP cc_start: 0.7356 (p0) cc_final: 0.7113 (p0) REVERT: A 3720 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 3740 LEU cc_start: 0.8506 (tp) cc_final: 0.8101 (tt) REVERT: A 3744 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 3885 MET cc_start: 0.8597 (mmm) cc_final: 0.8049 (mmm) REVERT: A 3913 GLU cc_start: 0.8144 (tp30) cc_final: 0.7510 (tt0) REVERT: A 3962 ASP cc_start: 0.7356 (t0) cc_final: 0.6568 (t70) REVERT: A 4168 ARG cc_start: 0.7746 (tpt-90) cc_final: 0.6887 (ttt180) REVERT: A 4377 MET cc_start: 0.7859 (ttm) cc_final: 0.7418 (ttp) REVERT: A 4573 ASN cc_start: 0.8478 (t0) cc_final: 0.8043 (t0) outliers start: 50 outliers final: 32 residues processed: 394 average time/residue: 0.1541 time to fit residues: 98.1294 Evaluate side-chains 310 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2588 HIS Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2599 SER Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2884 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 6 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 276 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A2003 ASN A2134 GLN A2282 HIS ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2296 GLN A2322 ASN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A4393 GLN A4530 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128940 restraints weight = 35992.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132036 restraints weight = 22710.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134130 restraints weight = 16765.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135327 restraints weight = 13725.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136375 restraints weight = 12103.362| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25108 Z= 0.132 Angle : 0.557 8.915 34050 Z= 0.281 Chirality : 0.040 0.229 3818 Planarity : 0.005 0.073 4361 Dihedral : 7.050 134.238 3410 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.18 % Allowed : 11.24 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.15), residues: 3026 helix: 2.13 (0.12), residues: 1773 sheet: -0.77 (0.32), residues: 256 loop : 0.44 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A3167 TYR 0.019 0.001 TYR A2748 PHE 0.020 0.002 PHE A3996 TRP 0.037 0.001 TRP A3489 HIS 0.005 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00298 (25108) covalent geometry : angle 0.55655 (34050) hydrogen bonds : bond 0.04145 ( 1460) hydrogen bonds : angle 4.14198 ( 4251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 0.930 Fit side-chains REVERT: A 1457 MET cc_start: 0.6333 (tpt) cc_final: 0.6115 (tpt) REVERT: A 1837 GLU cc_start: 0.6378 (mp0) cc_final: 0.6095 (mp0) REVERT: A 1876 GLN cc_start: 0.8026 (tp40) cc_final: 0.7659 (pm20) REVERT: A 2412 MET cc_start: 0.6619 (tpt) cc_final: 0.6129 (tpp) REVERT: A 2461 MET cc_start: 0.8438 (mtp) cc_final: 0.8068 (mtp) REVERT: A 2462 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8238 (mm) REVERT: A 2629 GLU cc_start: 0.7005 (mp0) cc_final: 0.6680 (mp0) REVERT: A 2658 TRP cc_start: 0.8226 (m100) cc_final: 0.7690 (m100) REVERT: A 2835 ASP cc_start: 0.7688 (m-30) cc_final: 0.7149 (m-30) REVERT: A 2987 ASN cc_start: 0.8311 (t0) cc_final: 0.7903 (p0) REVERT: A 3038 GLN cc_start: 0.7646 (mm110) cc_final: 0.7400 (mm-40) REVERT: A 3720 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 3740 LEU cc_start: 0.8491 (tp) cc_final: 0.8082 (tt) REVERT: A 3744 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 3913 GLU cc_start: 0.8133 (tp30) cc_final: 0.7505 (tt0) REVERT: A 3962 ASP cc_start: 0.7105 (t0) cc_final: 0.6441 (t70) REVERT: A 4168 ARG cc_start: 0.7720 (tpt-90) cc_final: 0.6854 (ttt180) REVERT: A 4377 MET cc_start: 0.7768 (ttm) cc_final: 0.7355 (ttp) REVERT: A 4481 ASP cc_start: 0.7247 (t70) cc_final: 0.7008 (t70) REVERT: A 4573 ASN cc_start: 0.8485 (t0) cc_final: 0.8035 (t0) outliers start: 31 outliers final: 19 residues processed: 321 average time/residue: 0.1581 time to fit residues: 83.4064 Evaluate side-chains 291 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2588 HIS Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 104 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 199 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A1481 GLN A2003 ASN A2290 ASN A2588 HIS A2621 ASN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2930 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127030 restraints weight = 33946.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129971 restraints weight = 22214.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131863 restraints weight = 16699.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132923 restraints weight = 13904.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133961 restraints weight = 12367.888| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25108 Z= 0.135 Angle : 0.548 10.575 34050 Z= 0.275 Chirality : 0.040 0.193 3818 Planarity : 0.004 0.078 4361 Dihedral : 6.674 122.998 3410 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 1.63 % Allowed : 12.24 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.16), residues: 3026 helix: 2.25 (0.12), residues: 1766 sheet: -0.79 (0.31), residues: 257 loop : 0.42 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A2844 TYR 0.019 0.001 TYR A2748 PHE 0.056 0.002 PHE A3094 TRP 0.025 0.001 TRP A1424 HIS 0.015 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00313 (25108) covalent geometry : angle 0.54778 (34050) hydrogen bonds : bond 0.03992 ( 1460) hydrogen bonds : angle 4.04720 ( 4251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 1417 MET cc_start: 0.6968 (mmm) cc_final: 0.6321 (mtt) REVERT: A 1457 MET cc_start: 0.6464 (tpt) cc_final: 0.6257 (tpt) REVERT: A 1872 TYR cc_start: 0.8274 (t80) cc_final: 0.7983 (t80) REVERT: A 1876 GLN cc_start: 0.8044 (tp40) cc_final: 0.7635 (pm20) REVERT: A 2412 MET cc_start: 0.6872 (tpt) cc_final: 0.6474 (tpp) REVERT: A 2461 MET cc_start: 0.8274 (mtp) cc_final: 0.7905 (mtp) REVERT: A 2462 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 2658 TRP cc_start: 0.8285 (m100) cc_final: 0.7806 (m100) REVERT: A 2835 ASP cc_start: 0.7797 (m-30) cc_final: 0.7046 (m-30) REVERT: A 2987 ASN cc_start: 0.8434 (t0) cc_final: 0.7967 (p0) REVERT: A 3026 TYR cc_start: 0.6911 (t80) cc_final: 0.6616 (t80) REVERT: A 3200 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6011 (t-90) REVERT: A 3666 ASP cc_start: 0.7389 (p0) cc_final: 0.6537 (t0) REVERT: A 3740 LEU cc_start: 0.8694 (tp) cc_final: 0.8370 (tt) REVERT: A 3744 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 3771 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7425 (tp30) REVERT: A 3885 MET cc_start: 0.8573 (mmm) cc_final: 0.7929 (mmm) REVERT: A 3913 GLU cc_start: 0.8163 (tp30) cc_final: 0.7541 (tt0) REVERT: A 3962 ASP cc_start: 0.6976 (t0) cc_final: 0.6356 (t70) REVERT: A 4168 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.6960 (ttt180) REVERT: A 4377 MET cc_start: 0.7790 (ttm) cc_final: 0.7420 (ttp) REVERT: A 4481 ASP cc_start: 0.7328 (t70) cc_final: 0.7082 (t70) REVERT: A 4573 ASN cc_start: 0.8536 (t0) cc_final: 0.8063 (t0) outliers start: 43 outliers final: 30 residues processed: 313 average time/residue: 0.1569 time to fit residues: 80.8672 Evaluate side-chains 286 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 118 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 206 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A2003 ASN A2377 ASN A2654 GLN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3038 GLN A3535 HIS A3865 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124499 restraints weight = 34711.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127319 restraints weight = 22753.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129224 restraints weight = 17193.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130333 restraints weight = 14306.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131279 restraints weight = 12732.381| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25108 Z= 0.146 Angle : 0.541 9.039 34050 Z= 0.274 Chirality : 0.040 0.224 3818 Planarity : 0.004 0.080 4361 Dihedral : 6.444 117.470 3410 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 1.92 % Allowed : 12.35 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.16), residues: 3026 helix: 2.30 (0.12), residues: 1759 sheet: -0.84 (0.31), residues: 259 loop : 0.45 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2844 TYR 0.040 0.001 TYR A1513 PHE 0.019 0.002 PHE A3094 TRP 0.033 0.001 TRP A1351 HIS 0.022 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00346 (25108) covalent geometry : angle 0.54074 (34050) hydrogen bonds : bond 0.03998 ( 1460) hydrogen bonds : angle 4.00266 ( 4251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8089 (mp10) cc_final: 0.7815 (mp10) REVERT: A 1417 MET cc_start: 0.7277 (mmm) cc_final: 0.6319 (mtm) REVERT: A 1663 SER cc_start: 0.8997 (p) cc_final: 0.8629 (m) REVERT: A 1745 TYR cc_start: 0.7619 (m-80) cc_final: 0.7356 (m-10) REVERT: A 1872 TYR cc_start: 0.8329 (t80) cc_final: 0.7960 (t80) REVERT: A 2446 ILE cc_start: 0.8627 (tp) cc_final: 0.8412 (tp) REVERT: A 2461 MET cc_start: 0.8459 (mtp) cc_final: 0.8060 (mtp) REVERT: A 2462 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 2785 THR cc_start: 0.8450 (p) cc_final: 0.8195 (p) REVERT: A 2835 ASP cc_start: 0.7810 (m-30) cc_final: 0.7103 (m-30) REVERT: A 3207 LYS cc_start: 0.6289 (tptp) cc_final: 0.5864 (tttt) REVERT: A 3639 GLU cc_start: 0.7816 (pm20) cc_final: 0.7528 (pm20) REVERT: A 3666 ASP cc_start: 0.7290 (p0) cc_final: 0.6493 (t0) REVERT: A 3740 LEU cc_start: 0.8787 (tp) cc_final: 0.8488 (tt) REVERT: A 3744 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 3771 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7463 (tp30) REVERT: A 3885 MET cc_start: 0.8554 (mmm) cc_final: 0.7983 (mmm) REVERT: A 3913 GLU cc_start: 0.8245 (tp30) cc_final: 0.7617 (tt0) REVERT: A 3962 ASP cc_start: 0.7055 (t0) cc_final: 0.6549 (t70) REVERT: A 4168 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7293 (ttt180) REVERT: A 4377 MET cc_start: 0.7765 (ttm) cc_final: 0.7317 (ttp) REVERT: A 4630 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7119 (mp0) outliers start: 51 outliers final: 39 residues processed: 316 average time/residue: 0.1541 time to fit residues: 79.7537 Evaluate side-chains 295 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3861 LYS Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 29 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 157 optimal weight: 0.0070 chunk 208 optimal weight: 0.0770 chunk 214 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A2003 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2463 HIS ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3069 ASN A3535 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4231 GLN A4393 GLN A4573 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126894 restraints weight = 34087.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129787 restraints weight = 22223.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131665 restraints weight = 16775.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133003 restraints weight = 13934.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133859 restraints weight = 12273.500| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25108 Z= 0.113 Angle : 0.521 9.143 34050 Z= 0.263 Chirality : 0.039 0.169 3818 Planarity : 0.004 0.076 4361 Dihedral : 6.269 112.559 3410 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.81 % Allowed : 12.98 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.16), residues: 3026 helix: 2.45 (0.12), residues: 1759 sheet: -0.87 (0.31), residues: 259 loop : 0.44 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2844 TYR 0.030 0.001 TYR A1513 PHE 0.014 0.001 PHE A3813 TRP 0.020 0.001 TRP A2234 HIS 0.004 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00254 (25108) covalent geometry : angle 0.52079 (34050) hydrogen bonds : bond 0.03730 ( 1460) hydrogen bonds : angle 3.90229 ( 4251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: A 1417 MET cc_start: 0.7272 (mmm) cc_final: 0.6130 (mtm) REVERT: A 1663 SER cc_start: 0.8965 (p) cc_final: 0.8621 (m) REVERT: A 1745 TYR cc_start: 0.7569 (m-80) cc_final: 0.7321 (m-10) REVERT: A 1872 TYR cc_start: 0.8263 (t80) cc_final: 0.7878 (t80) REVERT: A 2446 ILE cc_start: 0.8541 (tp) cc_final: 0.8282 (tp) REVERT: A 2462 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 2785 THR cc_start: 0.8443 (p) cc_final: 0.8187 (p) REVERT: A 2835 ASP cc_start: 0.7760 (m-30) cc_final: 0.7078 (m-30) REVERT: A 3030 MET cc_start: 0.6613 (mmm) cc_final: 0.5650 (mmm) REVERT: A 3200 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.5928 (t-90) REVERT: A 3207 LYS cc_start: 0.6273 (tptp) cc_final: 0.5881 (tttt) REVERT: A 3666 ASP cc_start: 0.7285 (p0) cc_final: 0.6477 (t0) REVERT: A 3740 LEU cc_start: 0.8786 (tp) cc_final: 0.8526 (tt) REVERT: A 3744 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 3771 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7509 (tp30) REVERT: A 3885 MET cc_start: 0.8533 (mmm) cc_final: 0.8140 (mmm) REVERT: A 3913 GLU cc_start: 0.8186 (tp30) cc_final: 0.7576 (tt0) REVERT: A 3962 ASP cc_start: 0.7082 (t0) cc_final: 0.6585 (t70) REVERT: A 4092 ARG cc_start: 0.6610 (mtp85) cc_final: 0.6176 (ttm-80) REVERT: A 4168 ARG cc_start: 0.7856 (tpt-90) cc_final: 0.7049 (ttt180) REVERT: A 4377 MET cc_start: 0.7743 (ttm) cc_final: 0.7324 (ttp) outliers start: 48 outliers final: 33 residues processed: 317 average time/residue: 0.1450 time to fit residues: 75.6606 Evaluate side-chains 294 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3124 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 185 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 174 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3535 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4393 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124238 restraints weight = 42506.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126685 restraints weight = 29250.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128013 restraints weight = 21121.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129032 restraints weight = 16471.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129184 restraints weight = 14898.393| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25108 Z= 0.151 Angle : 0.542 8.627 34050 Z= 0.273 Chirality : 0.040 0.160 3818 Planarity : 0.004 0.074 4361 Dihedral : 6.273 109.935 3410 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.95 % Favored : 97.98 % Rotamer: Outliers : 2.00 % Allowed : 13.09 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 3026 helix: 2.40 (0.12), residues: 1761 sheet: -0.95 (0.31), residues: 259 loop : 0.44 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2844 TYR 0.032 0.001 TYR A1513 PHE 0.016 0.002 PHE A1462 TRP 0.060 0.001 TRP A3489 HIS 0.005 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00362 (25108) covalent geometry : angle 0.54210 (34050) hydrogen bonds : bond 0.03912 ( 1460) hydrogen bonds : angle 3.96342 ( 4251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: A 1417 MET cc_start: 0.7234 (mmm) cc_final: 0.6300 (mtm) REVERT: A 1663 SER cc_start: 0.8968 (p) cc_final: 0.8628 (m) REVERT: A 1745 TYR cc_start: 0.7726 (m-80) cc_final: 0.7396 (m-10) REVERT: A 1872 TYR cc_start: 0.8435 (t80) cc_final: 0.8070 (t80) REVERT: A 2461 MET cc_start: 0.8538 (mtp) cc_final: 0.8118 (mtp) REVERT: A 2462 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 2785 THR cc_start: 0.8464 (p) cc_final: 0.8199 (p) REVERT: A 2835 ASP cc_start: 0.7916 (m-30) cc_final: 0.7189 (m-30) REVERT: A 3030 MET cc_start: 0.6705 (mmm) cc_final: 0.5846 (mmm) REVERT: A 3207 LYS cc_start: 0.6371 (tptp) cc_final: 0.5974 (tttt) REVERT: A 3666 ASP cc_start: 0.7359 (p0) cc_final: 0.6488 (t0) REVERT: A 3740 LEU cc_start: 0.8736 (tp) cc_final: 0.8479 (tt) REVERT: A 3744 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 3771 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 3885 MET cc_start: 0.8587 (mmm) cc_final: 0.8068 (mmm) REVERT: A 3962 ASP cc_start: 0.7371 (t0) cc_final: 0.6900 (t70) REVERT: A 4377 MET cc_start: 0.7802 (ttm) cc_final: 0.7332 (ttp) outliers start: 53 outliers final: 42 residues processed: 300 average time/residue: 0.1508 time to fit residues: 74.2173 Evaluate side-chains 292 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3124 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3861 LYS Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 224 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3535 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4393 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124756 restraints weight = 36567.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127756 restraints weight = 23508.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129766 restraints weight = 17545.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131069 restraints weight = 14436.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131887 restraints weight = 12723.085| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25108 Z= 0.120 Angle : 0.521 8.548 34050 Z= 0.262 Chirality : 0.039 0.152 3818 Planarity : 0.004 0.068 4361 Dihedral : 6.189 106.718 3410 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.02 % Rotamer: Outliers : 1.78 % Allowed : 13.39 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.16), residues: 3026 helix: 2.49 (0.12), residues: 1760 sheet: -0.95 (0.31), residues: 259 loop : 0.48 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2844 TYR 0.019 0.001 TYR A2748 PHE 0.017 0.001 PHE A3094 TRP 0.061 0.001 TRP A3489 HIS 0.004 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00277 (25108) covalent geometry : angle 0.52063 (34050) hydrogen bonds : bond 0.03730 ( 1460) hydrogen bonds : angle 3.89440 ( 4251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: A 1417 MET cc_start: 0.7268 (mmm) cc_final: 0.6309 (mtm) REVERT: A 1663 SER cc_start: 0.8999 (p) cc_final: 0.8687 (m) REVERT: A 1745 TYR cc_start: 0.7551 (m-80) cc_final: 0.7110 (m-10) REVERT: A 1872 TYR cc_start: 0.8283 (t80) cc_final: 0.7987 (t80) REVERT: A 2461 MET cc_start: 0.8516 (mtp) cc_final: 0.8092 (mtp) REVERT: A 2462 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8097 (mm) REVERT: A 2559 THR cc_start: 0.8161 (p) cc_final: 0.7747 (t) REVERT: A 2835 ASP cc_start: 0.7884 (m-30) cc_final: 0.7155 (m-30) REVERT: A 3030 MET cc_start: 0.6688 (mmm) cc_final: 0.5723 (mmm) REVERT: A 3207 LYS cc_start: 0.6334 (tptp) cc_final: 0.5925 (tttt) REVERT: A 3666 ASP cc_start: 0.7243 (p0) cc_final: 0.6414 (t0) REVERT: A 3740 LEU cc_start: 0.8698 (tp) cc_final: 0.8445 (tt) REVERT: A 3744 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 3755 GLU cc_start: 0.7389 (pp20) cc_final: 0.7097 (mp0) REVERT: A 3771 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7602 (tp30) REVERT: A 3885 MET cc_start: 0.8498 (mmm) cc_final: 0.8169 (mmm) REVERT: A 3962 ASP cc_start: 0.7437 (t0) cc_final: 0.7037 (t70) REVERT: A 4377 MET cc_start: 0.7770 (ttm) cc_final: 0.7336 (ttp) outliers start: 47 outliers final: 37 residues processed: 298 average time/residue: 0.1464 time to fit residues: 71.6773 Evaluate side-chains 291 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3124 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 271 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 244 optimal weight: 0.0570 chunk 217 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 237 optimal weight: 0.0010 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A1541 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2857 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4156 ASN A4393 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127479 restraints weight = 34140.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130347 restraints weight = 22334.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132285 restraints weight = 16871.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133408 restraints weight = 13982.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134313 restraints weight = 12429.562| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25108 Z= 0.106 Angle : 0.518 9.646 34050 Z= 0.261 Chirality : 0.038 0.187 3818 Planarity : 0.004 0.066 4361 Dihedral : 6.073 104.725 3410 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 13.91 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 3026 helix: 2.55 (0.12), residues: 1763 sheet: -0.96 (0.31), residues: 259 loop : 0.48 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2844 TYR 0.026 0.001 TYR A2350 PHE 0.038 0.001 PHE A3957 TRP 0.049 0.001 TRP A3489 HIS 0.004 0.001 HIS A1412 Details of bonding type rmsd covalent geometry : bond 0.00232 (25108) covalent geometry : angle 0.51780 (34050) hydrogen bonds : bond 0.03532 ( 1460) hydrogen bonds : angle 3.83403 ( 4251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: A 1417 MET cc_start: 0.7210 (mmm) cc_final: 0.6294 (mtm) REVERT: A 1663 SER cc_start: 0.8924 (p) cc_final: 0.8627 (m) REVERT: A 1745 TYR cc_start: 0.7348 (m-80) cc_final: 0.7012 (m-10) REVERT: A 1872 TYR cc_start: 0.8275 (t80) cc_final: 0.7953 (t80) REVERT: A 2287 ILE cc_start: 0.8820 (mm) cc_final: 0.8608 (mt) REVERT: A 2462 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 2559 THR cc_start: 0.8153 (p) cc_final: 0.7764 (t) REVERT: A 2835 ASP cc_start: 0.7885 (m-30) cc_final: 0.7140 (m-30) REVERT: A 3030 MET cc_start: 0.6679 (mmm) cc_final: 0.5711 (mmm) REVERT: A 3207 LYS cc_start: 0.6346 (tptp) cc_final: 0.5929 (tttt) REVERT: A 3666 ASP cc_start: 0.7301 (p0) cc_final: 0.6490 (t0) REVERT: A 3740 LEU cc_start: 0.8840 (tp) cc_final: 0.8585 (tt) REVERT: A 3744 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 3755 GLU cc_start: 0.7214 (pp20) cc_final: 0.6914 (mp0) REVERT: A 3771 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7527 (tp30) REVERT: A 3885 MET cc_start: 0.8409 (mmm) cc_final: 0.8149 (mmm) REVERT: A 3962 ASP cc_start: 0.7314 (t0) cc_final: 0.7004 (t70) REVERT: A 4377 MET cc_start: 0.7717 (ttm) cc_final: 0.7295 (ttp) outliers start: 45 outliers final: 35 residues processed: 295 average time/residue: 0.1511 time to fit residues: 73.8478 Evaluate side-chains 291 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2373 MET Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3124 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 181 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 270 optimal weight: 0.2980 chunk 165 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2857 HIS A3534 HIS A3931 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4393 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125701 restraints weight = 47867.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128743 restraints weight = 34165.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129989 restraints weight = 23230.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130810 restraints weight = 16555.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130983 restraints weight = 15145.021| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25108 Z= 0.118 Angle : 0.518 8.637 34050 Z= 0.261 Chirality : 0.039 0.152 3818 Planarity : 0.004 0.065 4361 Dihedral : 6.030 103.726 3410 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.48 % Allowed : 14.13 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.16), residues: 3026 helix: 2.56 (0.12), residues: 1763 sheet: -0.92 (0.31), residues: 259 loop : 0.51 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2844 TYR 0.021 0.001 TYR A2350 PHE 0.028 0.001 PHE A3957 TRP 0.045 0.001 TRP A3489 HIS 0.005 0.001 HIS A3534 Details of bonding type rmsd covalent geometry : bond 0.00271 (25108) covalent geometry : angle 0.51814 (34050) hydrogen bonds : bond 0.03592 ( 1460) hydrogen bonds : angle 3.83097 ( 4251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: A 1663 SER cc_start: 0.8992 (p) cc_final: 0.8693 (m) REVERT: A 1745 TYR cc_start: 0.7518 (m-80) cc_final: 0.7230 (m-10) REVERT: A 1872 TYR cc_start: 0.8358 (t80) cc_final: 0.7975 (t80) REVERT: A 2287 ILE cc_start: 0.8864 (mm) cc_final: 0.8618 (mt) REVERT: A 2461 MET cc_start: 0.8484 (mtp) cc_final: 0.8039 (mtp) REVERT: A 2462 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 2559 THR cc_start: 0.8216 (p) cc_final: 0.7783 (t) REVERT: A 2835 ASP cc_start: 0.7907 (m-30) cc_final: 0.7158 (m-30) REVERT: A 3030 MET cc_start: 0.6613 (mmm) cc_final: 0.5606 (mmm) REVERT: A 3207 LYS cc_start: 0.6462 (tptp) cc_final: 0.5979 (tttt) REVERT: A 3666 ASP cc_start: 0.7465 (p0) cc_final: 0.6348 (t0) REVERT: A 3740 LEU cc_start: 0.8854 (tp) cc_final: 0.8607 (tt) REVERT: A 3744 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 3755 GLU cc_start: 0.7307 (pp20) cc_final: 0.6832 (mp0) REVERT: A 3771 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7518 (tp30) REVERT: A 3885 MET cc_start: 0.8476 (mmm) cc_final: 0.8186 (mmm) REVERT: A 3962 ASP cc_start: 0.7474 (t0) cc_final: 0.7138 (t70) REVERT: A 4377 MET cc_start: 0.7769 (ttm) cc_final: 0.7323 (ttp) outliers start: 39 outliers final: 34 residues processed: 283 average time/residue: 0.1462 time to fit residues: 69.0364 Evaluate side-chains 288 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1972 SER Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2373 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2639 CYS Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3124 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3613 SER Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4031 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 213 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 276 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2857 HIS A3534 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125743 restraints weight = 42850.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127495 restraints weight = 28420.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129121 restraints weight = 20554.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130479 restraints weight = 16810.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130752 restraints weight = 15176.356| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25108 Z= 0.123 Angle : 0.522 8.551 34050 Z= 0.263 Chirality : 0.039 0.146 3818 Planarity : 0.004 0.070 4361 Dihedral : 6.030 102.116 3410 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 14.16 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.16), residues: 3026 helix: 2.55 (0.12), residues: 1763 sheet: -0.92 (0.31), residues: 259 loop : 0.50 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2844 TYR 0.019 0.001 TYR A2748 PHE 0.029 0.001 PHE A3957 TRP 0.042 0.001 TRP A3489 HIS 0.005 0.001 HIS A1412 Details of bonding type rmsd covalent geometry : bond 0.00287 (25108) covalent geometry : angle 0.52226 (34050) hydrogen bonds : bond 0.03632 ( 1460) hydrogen bonds : angle 3.83423 ( 4251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4307.09 seconds wall clock time: 75 minutes 10.49 seconds (4510.49 seconds total)