Starting phenix.real_space_refine on Sat May 24 04:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmd_44696/05_2025/9bmd_44696.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.036 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 122 5.16 5 C 15631 2.51 5 N 4250 2.21 5 O 4585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24603 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24479 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3038, 24471 Classifications: {'peptide': 3038} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2904} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 3038, 24471 Classifications: {'peptide': 3038} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2904} Chain breaks: 4 bond proxies already assigned to first conformer: 24980 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: 24.08, per 1000 atoms: 0.98 Number of scatterers: 24603 At special positions: 0 Unit cell: (121.275, 155.1, 179.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 11 15.00 Mg 4 11.99 O 4585 8.00 N 4250 7.00 C 15631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.55 Conformation dependent library (CDL) restraints added in 6.1 seconds 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5782 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 63.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1420 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.651A 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: 4.303A 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: 3.733A 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 removed outlier: 4.068A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) 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 1828 removed outlier: 3.518A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1984 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 2425 through 2428 removed outlier: 3.832A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.604A 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: 4.121A 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 2757 Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.736A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.139A 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: 3.523A 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: 4.306A 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: 3.704A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3517 removed outlier: 4.747A 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: 4.072A 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: 3.596A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.615A 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 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.161A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.512A 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: 4.094A 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 4013 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: 3.927A 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: 4.473A 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: 4.493A 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 4406 removed outlier: 4.168A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4440 removed outlier: 3.516A pdb=" N LYS A4422 " --> pdb=" O LYS A4418 " (cutoff:3.500A) 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: 3.600A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.411A 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: 6.539A 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: 8.461A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.256A 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: 6.749A 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: 7.684A 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) 1459 hydrogen bonds defined for protein. 4254 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: 14.54 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8115 1.34 - 1.46: 4851 1.46 - 1.58: 11936 1.58 - 1.70: 14 1.70 - 1.81: 210 Bond restraints: 25126 Sorted by residual: bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N LEU A2080 " pdb=" CA LEU A2080 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.20e+00 bond pdb=" N ILE A4521 " pdb=" CA ILE A4521 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N ILE A1571 " pdb=" CA ILE A1571 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.73e+00 bond pdb=" N VAL A1563 " pdb=" CA VAL A1563 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.38e+00 ... (remaining 25121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 33646 2.24 - 4.48: 390 4.48 - 6.72: 32 6.72 - 8.96: 3 8.96 - 11.20: 1 Bond angle restraints: 34072 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=" C GLU A2904 " pdb=" CA GLU A2904 " pdb=" CB GLU A2904 " ideal model delta sigma weight residual 116.34 110.64 5.70 1.40e+00 5.10e-01 1.66e+01 angle pdb=" CA LEU A2581 " pdb=" CB LEU A2581 " pdb=" CG LEU A2581 " ideal model delta sigma weight residual 116.30 127.50 -11.20 3.50e+00 8.16e-02 1.02e+01 angle pdb=" N LYS A2074 " pdb=" CA LYS A2074 " pdb=" C LYS A2074 " ideal model delta sigma weight residual 111.36 107.96 3.40 1.09e+00 8.42e-01 9.74e+00 angle pdb=" N GLU A3490 " pdb=" CA GLU A3490 " pdb=" CB GLU A3490 " ideal model delta sigma weight residual 110.16 114.76 -4.60 1.48e+00 4.57e-01 9.66e+00 ... (remaining 34067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 14678 28.57 - 57.13: 495 57.13 - 85.70: 105 85.70 - 114.26: 8 114.26 - 142.83: 1 Dihedral angle restraints: 15287 sinusoidal: 6387 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 -59.72 142.83 1 3.00e+01 1.11e-03 1.92e+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 -26.28 109.39 1 3.00e+01 1.11e-03 1.42e+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 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 15284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2833 0.041 - 0.083: 731 0.083 - 0.124: 230 0.124 - 0.166: 19 0.166 - 0.207: 4 Chirality restraints: 3817 Sorted by residual: chirality pdb=" CA ILE A1571 " pdb=" N ILE A1571 " pdb=" C ILE A1571 " pdb=" CB ILE A1571 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A4521 " pdb=" N ILE A4521 " pdb=" C ILE A4521 " pdb=" CB ILE A4521 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL A1563 " pdb=" N VAL A1563 " pdb=" C VAL A1563 " pdb=" CB VAL A1563 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 3814 not shown) Planarity restraints: 4364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3591 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A3592 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A3592 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3592 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A4117 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A4118 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A4118 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A4118 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1539 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ASP A1539 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP A1539 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A1540 " -0.013 2.00e-02 2.50e+03 ... (remaining 4361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 165 2.54 - 3.13: 19486 3.13 - 3.72: 39883 3.72 - 4.31: 55917 4.31 - 4.90: 94306 Nonbonded interactions: 209757 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 1.977 2.170 nonbonded pdb=" O3G ANP A4703 " pdb="MG MG A4707 " model vdw 2.021 2.170 nonbonded pdb=" OG1 THR A2944 " pdb="MG MG A4708 " model vdw 2.062 2.170 ... (remaining 209752 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 individual isotropic 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 77.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25126 Z= 0.185 Angle : 0.564 11.201 34072 Z= 0.319 Chirality : 0.041 0.207 3817 Planarity : 0.005 0.082 4364 Dihedral : 14.586 142.830 9505 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.75 % Favored : 98.18 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3029 helix: 1.41 (0.12), residues: 1761 sheet: -0.83 (0.32), residues: 236 loop : 0.36 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4376 HIS 0.005 0.001 HIS A1695 PHE 0.024 0.001 PHE A3813 TYR 0.023 0.001 TYR A3836 ARG 0.007 0.000 ARG A4591 Details of bonding type rmsd hydrogen bonds : bond 0.11806 ( 1459) hydrogen bonds : angle 5.65027 ( 4254) covalent geometry : bond 0.00355 (25126) covalent geometry : angle 0.56372 (34072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 1998 THR cc_start: 0.8648 (p) cc_final: 0.8388 (p) REVERT: A 2308 ASP cc_start: 0.6413 (m-30) cc_final: 0.6124 (m-30) REVERT: A 2962 LYS cc_start: 0.7620 (mtmm) cc_final: 0.6596 (mmtt) REVERT: A 3014 ASN cc_start: 0.7938 (t0) cc_final: 0.7552 (m-40) REVERT: A 3068 MET cc_start: 0.8453 (ptm) cc_final: 0.7880 (ptp) REVERT: A 4404 ASN cc_start: 0.4765 (m110) cc_final: 0.4324 (m110) REVERT: A 4481 ASP cc_start: 0.6894 (m-30) cc_final: 0.6562 (m-30) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 1.5375 time to fit residues: 635.4862 Evaluate side-chains 272 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 237 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1566 GLN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 HIS A2491 GLN A2752 ASN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121970 restraints weight = 32916.583| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.01 r_work: 0.3262 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25126 Z= 0.134 Angle : 0.536 9.820 34072 Z= 0.274 Chirality : 0.040 0.141 3817 Planarity : 0.005 0.068 4364 Dihedral : 7.893 140.027 3415 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.59 % Favored : 98.35 % Rotamer: Outliers : 1.04 % Allowed : 7.40 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3029 helix: 2.00 (0.12), residues: 1775 sheet: -0.64 (0.33), residues: 222 loop : 0.40 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.012 0.001 HIS A3200 PHE 0.022 0.001 PHE A3813 TYR 0.025 0.001 TYR A2748 ARG 0.011 0.001 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1459) hydrogen bonds : angle 4.30562 ( 4254) covalent geometry : bond 0.00301 (25126) covalent geometry : angle 0.53578 (34072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 2.719 Fit side-chains REVERT: A 1514 LYS cc_start: 0.7563 (mptt) cc_final: 0.7102 (mptt) REVERT: A 1602 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 1937 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 2060 ARG cc_start: 0.7804 (ptt90) cc_final: 0.7376 (mpt90) REVERT: A 2174 GLU cc_start: 0.5839 (tp30) cc_final: 0.5543 (mm-30) REVERT: A 2212 GLN cc_start: 0.7003 (pt0) cc_final: 0.6725 (pt0) REVERT: A 2308 ASP cc_start: 0.6488 (m-30) cc_final: 0.6062 (m-30) REVERT: A 2885 ASP cc_start: 0.7520 (t0) cc_final: 0.7262 (t0) REVERT: A 2902 GLU cc_start: 0.6798 (mp0) cc_final: 0.6393 (mp0) REVERT: A 2962 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6168 (mmtt) REVERT: A 3007 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7882 (ttm-80) REVERT: A 3014 ASN cc_start: 0.7829 (t0) cc_final: 0.7130 (m-40) REVERT: A 3049 GLU cc_start: 0.7132 (tp30) cc_final: 0.6899 (pt0) REVERT: A 3068 MET cc_start: 0.8186 (ptm) cc_final: 0.7308 (ptp) REVERT: A 3792 GLN cc_start: 0.7339 (tp40) cc_final: 0.6964 (mp10) REVERT: A 4404 ASN cc_start: 0.3973 (m110) cc_final: 0.3563 (m110) REVERT: A 4526 GLN cc_start: 0.6942 (mt0) cc_final: 0.6683 (mt0) outliers start: 27 outliers final: 7 residues processed: 317 average time/residue: 1.4526 time to fit residues: 528.8073 Evaluate side-chains 283 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 275 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 4236 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 140 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 290 optimal weight: 0.5980 chunk 186 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1832 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN A3772 ASN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121388 restraints weight = 31087.091| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.04 r_work: 0.3277 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25126 Z= 0.129 Angle : 0.510 8.188 34072 Z= 0.259 Chirality : 0.039 0.145 3817 Planarity : 0.004 0.063 4364 Dihedral : 7.396 140.637 3415 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 8.91 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3029 helix: 2.11 (0.12), residues: 1775 sheet: -0.59 (0.34), residues: 224 loop : 0.41 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.011 0.001 HIS A3200 PHE 0.021 0.001 PHE A3813 TYR 0.022 0.001 TYR A2748 ARG 0.013 0.001 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1459) hydrogen bonds : angle 4.18471 ( 4254) covalent geometry : bond 0.00298 (25126) covalent geometry : angle 0.51014 (34072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 2.866 Fit side-chains revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 1649 LYS cc_start: 0.8207 (mttt) cc_final: 0.7930 (ttmm) REVERT: A 1937 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (t0) REVERT: A 2060 ARG cc_start: 0.7889 (ptt90) cc_final: 0.7398 (mpt90) REVERT: A 2169 GLN cc_start: 0.7055 (tp40) cc_final: 0.6630 (mm-40) REVERT: A 2308 ASP cc_start: 0.6400 (m-30) cc_final: 0.6069 (m-30) REVERT: A 2510 MET cc_start: 0.7514 (mmm) cc_final: 0.6810 (mmt) REVERT: A 2902 GLU cc_start: 0.6754 (mp0) cc_final: 0.6501 (mp0) REVERT: A 3007 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7814 (ttm-80) REVERT: A 3014 ASN cc_start: 0.7855 (t0) cc_final: 0.7087 (m-40) REVERT: A 3043 MET cc_start: 0.7925 (ptp) cc_final: 0.6883 (ppp) REVERT: A 3049 GLU cc_start: 0.7137 (tp30) cc_final: 0.6870 (pt0) REVERT: A 3068 MET cc_start: 0.8200 (ptm) cc_final: 0.7316 (ptp) REVERT: A 3792 GLN cc_start: 0.7382 (tp40) cc_final: 0.6990 (mp10) REVERT: A 3968 GLN cc_start: 0.7904 (mt0) cc_final: 0.7643 (mm-40) REVERT: A 4404 ASN cc_start: 0.4070 (m110) cc_final: 0.3631 (m110) outliers start: 34 outliers final: 13 residues processed: 315 average time/residue: 1.4347 time to fit residues: 522.5838 Evaluate side-chains 287 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 273 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 297 optimal weight: 0.0870 chunk 274 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2886 GLN A3772 ASN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118653 restraints weight = 38228.416| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.21 r_work: 0.3227 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25126 Z= 0.155 Angle : 0.531 8.769 34072 Z= 0.268 Chirality : 0.040 0.149 3817 Planarity : 0.004 0.067 4364 Dihedral : 7.191 129.024 3415 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer: Outliers : 1.41 % Allowed : 10.28 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.15), residues: 3029 helix: 2.08 (0.12), residues: 1770 sheet: -0.61 (0.34), residues: 224 loop : 0.36 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.010 0.001 HIS A3200 PHE 0.024 0.002 PHE A3813 TYR 0.018 0.001 TYR A2748 ARG 0.012 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1459) hydrogen bonds : angle 4.20037 ( 4254) covalent geometry : bond 0.00370 (25126) covalent geometry : angle 0.53061 (34072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 3.108 Fit side-chains revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 1649 LYS cc_start: 0.8236 (mttt) cc_final: 0.7914 (ttmm) REVERT: A 1799 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: A 1937 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 1998 THR cc_start: 0.8301 (p) cc_final: 0.8071 (p) REVERT: A 2060 ARG cc_start: 0.7929 (ptt90) cc_final: 0.7426 (mpt90) REVERT: A 2169 GLN cc_start: 0.7118 (tp40) cc_final: 0.6694 (mm-40) REVERT: A 2222 MET cc_start: 0.8632 (mtm) cc_final: 0.8284 (mtt) REVERT: A 2308 ASP cc_start: 0.6443 (m-30) cc_final: 0.6126 (m-30) REVERT: A 2510 MET cc_start: 0.7691 (mmm) cc_final: 0.7013 (mmt) REVERT: A 2814 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 2885 ASP cc_start: 0.7575 (t0) cc_final: 0.7322 (t0) REVERT: A 2902 GLU cc_start: 0.6783 (mp0) cc_final: 0.6543 (mp0) REVERT: A 3007 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7871 (ttm-80) REVERT: A 3014 ASN cc_start: 0.7850 (t0) cc_final: 0.7102 (m-40) REVERT: A 3043 MET cc_start: 0.7884 (ptp) cc_final: 0.6834 (ppp) REVERT: A 3049 GLU cc_start: 0.7191 (tp30) cc_final: 0.6951 (mt-10) REVERT: A 3068 MET cc_start: 0.8284 (ptm) cc_final: 0.7384 (ptp) REVERT: A 3654 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6676 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7486 (tp40) cc_final: 0.7057 (mp10) REVERT: A 3885 MET cc_start: 0.8504 (mmm) cc_final: 0.8092 (mmm) REVERT: A 3968 GLN cc_start: 0.7948 (mt0) cc_final: 0.7592 (mm-40) REVERT: A 4022 GLU cc_start: 0.7661 (mp0) cc_final: 0.7393 (mm-30) REVERT: A 4404 ASN cc_start: 0.4226 (m110) cc_final: 0.3760 (m110) outliers start: 37 outliers final: 17 residues processed: 304 average time/residue: 1.4685 time to fit residues: 515.1699 Evaluate side-chains 285 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 239 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119162 restraints weight = 33130.671| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.23 r_work: 0.3235 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25126 Z= 0.134 Angle : 0.510 8.789 34072 Z= 0.258 Chirality : 0.039 0.148 3817 Planarity : 0.004 0.070 4364 Dihedral : 6.923 119.582 3415 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.37 % Allowed : 10.91 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.15), residues: 3029 helix: 2.13 (0.12), residues: 1770 sheet: -0.71 (0.33), residues: 234 loop : 0.39 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.012 0.001 HIS A3200 PHE 0.021 0.001 PHE A3813 TYR 0.021 0.001 TYR A2748 ARG 0.013 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1459) hydrogen bonds : angle 4.12761 ( 4254) covalent geometry : bond 0.00313 (25126) covalent geometry : angle 0.50995 (34072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 2.730 Fit side-chains revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 1649 LYS cc_start: 0.8144 (mttt) cc_final: 0.7899 (ttmm) REVERT: A 1799 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: A 1937 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (t0) REVERT: A 2060 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7414 (mpt90) REVERT: A 2169 GLN cc_start: 0.7113 (tp40) cc_final: 0.6680 (mm-40) REVERT: A 2222 MET cc_start: 0.8630 (mtm) cc_final: 0.8354 (mtt) REVERT: A 2308 ASP cc_start: 0.6387 (m-30) cc_final: 0.6042 (m-30) REVERT: A 2510 MET cc_start: 0.7554 (mmm) cc_final: 0.6885 (mmt) REVERT: A 2522 THR cc_start: 0.7949 (t) cc_final: 0.7607 (t) REVERT: A 2712 CYS cc_start: 0.8464 (m) cc_final: 0.7963 (p) REVERT: A 2814 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 2902 GLU cc_start: 0.6717 (mp0) cc_final: 0.6495 (mp0) REVERT: A 3014 ASN cc_start: 0.7818 (t0) cc_final: 0.7049 (m-40) REVERT: A 3043 MET cc_start: 0.7871 (ptp) cc_final: 0.6821 (ppp) REVERT: A 3049 GLU cc_start: 0.7242 (tp30) cc_final: 0.6992 (mt-10) REVERT: A 3068 MET cc_start: 0.8226 (ptm) cc_final: 0.7318 (ptp) REVERT: A 3792 GLN cc_start: 0.7464 (tp40) cc_final: 0.7032 (mp10) REVERT: A 3968 GLN cc_start: 0.7884 (mt0) cc_final: 0.7598 (mm-40) REVERT: A 4022 GLU cc_start: 0.7644 (mp0) cc_final: 0.7387 (mm-30) REVERT: A 4404 ASN cc_start: 0.4137 (m110) cc_final: 0.3670 (m110) REVERT: A 4573 ASN cc_start: 0.7202 (t0) cc_final: 0.6921 (m110) outliers start: 36 outliers final: 18 residues processed: 303 average time/residue: 1.4087 time to fit residues: 492.7603 Evaluate side-chains 298 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 283 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 300 optimal weight: 0.9980 chunk 276 optimal weight: 0.0050 chunk 279 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 238 optimal weight: 0.0980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2215 GLN A2322 ASN ** A2667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124017 restraints weight = 31261.982| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.03 r_work: 0.3308 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25126 Z= 0.106 Angle : 0.489 9.468 34072 Z= 0.247 Chirality : 0.038 0.140 3817 Planarity : 0.004 0.072 4364 Dihedral : 6.498 112.078 3415 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 11.69 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.15), residues: 3029 helix: 2.29 (0.12), residues: 1768 sheet: -0.66 (0.32), residues: 240 loop : 0.42 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.013 0.001 HIS A3200 PHE 0.018 0.001 PHE A3813 TYR 0.016 0.001 TYR A2748 ARG 0.014 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1459) hydrogen bonds : angle 4.00229 ( 4254) covalent geometry : bond 0.00232 (25126) covalent geometry : angle 0.48921 (34072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 2.883 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: A 1602 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 1649 LYS cc_start: 0.8189 (mttt) cc_final: 0.7883 (ttmm) REVERT: A 1914 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7317 (mm-30) REVERT: A 2060 ARG cc_start: 0.7907 (ptt90) cc_final: 0.7416 (mpt90) REVERT: A 2169 GLN cc_start: 0.7135 (tp40) cc_final: 0.6709 (mm-40) REVERT: A 2222 MET cc_start: 0.8531 (mtm) cc_final: 0.8252 (mtp) REVERT: A 2308 ASP cc_start: 0.6263 (m-30) cc_final: 0.5946 (m-30) REVERT: A 2473 ASN cc_start: 0.7239 (m-40) cc_final: 0.6963 (m-40) REVERT: A 2510 MET cc_start: 0.7459 (mmm) cc_final: 0.6804 (mmt) REVERT: A 2522 THR cc_start: 0.7962 (t) cc_final: 0.7595 (t) REVERT: A 2712 CYS cc_start: 0.8318 (m) cc_final: 0.7823 (p) REVERT: A 2814 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 2885 ASP cc_start: 0.7515 (t0) cc_final: 0.7280 (t0) REVERT: A 2902 GLU cc_start: 0.6749 (mp0) cc_final: 0.6527 (mp0) REVERT: A 3014 ASN cc_start: 0.7844 (t0) cc_final: 0.7088 (m-40) REVERT: A 3043 MET cc_start: 0.7784 (ptp) cc_final: 0.6798 (ppp) REVERT: A 3049 GLU cc_start: 0.7190 (tp30) cc_final: 0.6946 (mt-10) REVERT: A 3068 MET cc_start: 0.8175 (ptm) cc_final: 0.7337 (ptp) REVERT: A 3502 THR cc_start: 0.7713 (m) cc_final: 0.7404 (t) REVERT: A 3654 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6672 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7458 (tp40) cc_final: 0.7055 (mp10) REVERT: A 3800 GLN cc_start: 0.7615 (tt0) cc_final: 0.7164 (tm-30) REVERT: A 3968 GLN cc_start: 0.7857 (mt0) cc_final: 0.7578 (mm-40) REVERT: A 4022 GLU cc_start: 0.7512 (mp0) cc_final: 0.7290 (mm-30) REVERT: A 4271 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7930 (tmm-80) REVERT: A 4404 ASN cc_start: 0.4090 (m110) cc_final: 0.3613 (m110) REVERT: A 4481 ASP cc_start: 0.6356 (m-30) cc_final: 0.5956 (m-30) REVERT: A 4573 ASN cc_start: 0.6917 (t0) cc_final: 0.6660 (m110) outliers start: 27 outliers final: 12 residues processed: 310 average time/residue: 1.4329 time to fit residues: 512.8685 Evaluate side-chains 290 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3744 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 72 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121657 restraints weight = 38558.164| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.44 r_work: 0.3226 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25126 Z= 0.126 Angle : 0.510 12.027 34072 Z= 0.255 Chirality : 0.039 0.189 3817 Planarity : 0.004 0.069 4364 Dihedral : 6.494 111.826 3415 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.02 % Rotamer: Outliers : 1.33 % Allowed : 11.95 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.15), residues: 3029 helix: 2.25 (0.12), residues: 1771 sheet: -0.58 (0.33), residues: 230 loop : 0.42 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.012 0.001 HIS A3200 PHE 0.020 0.001 PHE A3813 TYR 0.021 0.001 TYR A2748 ARG 0.015 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1459) hydrogen bonds : angle 4.02261 ( 4254) covalent geometry : bond 0.00293 (25126) covalent geometry : angle 0.50954 (34072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 1649 LYS cc_start: 0.8194 (mttt) cc_final: 0.7890 (ttmm) REVERT: A 1914 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 2060 ARG cc_start: 0.7886 (ptt90) cc_final: 0.7418 (mpt90) REVERT: A 2169 GLN cc_start: 0.7099 (tp40) cc_final: 0.6702 (mm-40) REVERT: A 2308 ASP cc_start: 0.6259 (m-30) cc_final: 0.5969 (m-30) REVERT: A 2473 ASN cc_start: 0.7262 (m-40) cc_final: 0.7027 (m-40) REVERT: A 2510 MET cc_start: 0.7451 (mmm) cc_final: 0.6778 (mmt) REVERT: A 2522 THR cc_start: 0.7969 (t) cc_final: 0.7609 (t) REVERT: A 2712 CYS cc_start: 0.8212 (m) cc_final: 0.7738 (p) REVERT: A 2814 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 2885 ASP cc_start: 0.7533 (t0) cc_final: 0.7325 (t0) REVERT: A 2902 GLU cc_start: 0.6712 (mp0) cc_final: 0.6386 (mp0) REVERT: A 3008 MET cc_start: 0.7954 (tpt) cc_final: 0.7740 (tpp) REVERT: A 3014 ASN cc_start: 0.7807 (t0) cc_final: 0.7072 (m-40) REVERT: A 3043 MET cc_start: 0.7738 (ptp) cc_final: 0.6775 (ppp) REVERT: A 3049 GLU cc_start: 0.7158 (tp30) cc_final: 0.6938 (mt-10) REVERT: A 3068 MET cc_start: 0.8150 (ptm) cc_final: 0.7312 (ptp) REVERT: A 3654 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6633 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7418 (tp40) cc_final: 0.7051 (mp10) REVERT: A 3968 GLN cc_start: 0.7843 (mt0) cc_final: 0.7570 (mm-40) REVERT: A 4108 GLN cc_start: 0.6382 (mm-40) cc_final: 0.5431 (mt0) REVERT: A 4128 MET cc_start: 0.8096 (mtt) cc_final: 0.7784 (mtm) REVERT: A 4315 THR cc_start: 0.7844 (p) cc_final: 0.7560 (t) REVERT: A 4404 ASN cc_start: 0.4135 (m110) cc_final: 0.3671 (m110) outliers start: 35 outliers final: 16 residues processed: 303 average time/residue: 1.5050 time to fit residues: 525.3268 Evaluate side-chains 291 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3744 GLN Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 38 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118264 restraints weight = 30928.465| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.11 r_work: 0.3225 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25126 Z= 0.158 Angle : 0.540 14.124 34072 Z= 0.271 Chirality : 0.040 0.271 3817 Planarity : 0.004 0.074 4364 Dihedral : 6.634 112.610 3415 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 1.22 % Allowed : 12.39 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3029 helix: 2.16 (0.12), residues: 1771 sheet: -0.61 (0.33), residues: 230 loop : 0.41 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2234 HIS 0.011 0.001 HIS A3200 PHE 0.022 0.002 PHE A3813 TYR 0.023 0.001 TYR A2748 ARG 0.017 0.001 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 1459) hydrogen bonds : angle 4.11953 ( 4254) covalent geometry : bond 0.00378 (25126) covalent geometry : angle 0.53969 (34072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 2.947 Fit side-chains revert: symmetry clash REVERT: A 1417 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4978 (tpp) REVERT: A 1602 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 1649 LYS cc_start: 0.8225 (mttt) cc_final: 0.7880 (ttmm) REVERT: A 1914 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 1998 THR cc_start: 0.8306 (p) cc_final: 0.8071 (p) REVERT: A 2060 ARG cc_start: 0.7938 (ptt90) cc_final: 0.7416 (mpt90) REVERT: A 2169 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6681 (mm-40) REVERT: A 2308 ASP cc_start: 0.6315 (m-30) cc_final: 0.6021 (m-30) REVERT: A 2444 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 2510 MET cc_start: 0.7597 (mmm) cc_final: 0.6912 (mmt) REVERT: A 2522 THR cc_start: 0.7962 (t) cc_final: 0.7595 (t) REVERT: A 2712 CYS cc_start: 0.8457 (m) cc_final: 0.7960 (p) REVERT: A 2814 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: A 2885 ASP cc_start: 0.7545 (t0) cc_final: 0.7312 (t0) REVERT: A 2902 GLU cc_start: 0.6751 (mp0) cc_final: 0.6441 (mp0) REVERT: A 3008 MET cc_start: 0.7996 (tpt) cc_final: 0.7686 (tpp) REVERT: A 3014 ASN cc_start: 0.7772 (t0) cc_final: 0.7038 (m-40) REVERT: A 3043 MET cc_start: 0.7708 (ptp) cc_final: 0.6718 (ppp) REVERT: A 3049 GLU cc_start: 0.7249 (tp30) cc_final: 0.7000 (mt-10) REVERT: A 3068 MET cc_start: 0.8309 (ptm) cc_final: 0.7374 (ptp) REVERT: A 3654 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6591 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7490 (tp40) cc_final: 0.7063 (mp10) REVERT: A 3968 GLN cc_start: 0.7871 (mt0) cc_final: 0.7585 (mm-40) REVERT: A 4128 MET cc_start: 0.8201 (mtt) cc_final: 0.7941 (mtm) REVERT: A 4209 GLU cc_start: 0.7556 (tp30) cc_final: 0.7320 (tp30) REVERT: A 4283 LYS cc_start: 0.8446 (mptt) cc_final: 0.8153 (mmtm) REVERT: A 4315 THR cc_start: 0.7900 (p) cc_final: 0.7630 (t) REVERT: A 4404 ASN cc_start: 0.4201 (m110) cc_final: 0.3727 (m110) outliers start: 32 outliers final: 18 residues processed: 294 average time/residue: 1.4739 time to fit residues: 498.5733 Evaluate side-chains 294 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 2169 GLN Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 240 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 299 optimal weight: 0.0980 chunk 182 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN ** A4466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119768 restraints weight = 29060.092| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.09 r_work: 0.3258 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25126 Z= 0.121 Angle : 0.511 14.560 34072 Z= 0.257 Chirality : 0.039 0.147 3817 Planarity : 0.004 0.074 4364 Dihedral : 6.461 112.727 3415 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.11 % Allowed : 12.80 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.15), residues: 3029 helix: 2.24 (0.12), residues: 1771 sheet: -0.61 (0.33), residues: 230 loop : 0.42 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2234 HIS 0.012 0.001 HIS A3200 PHE 0.019 0.001 PHE A3813 TYR 0.021 0.001 TYR A2748 ARG 0.016 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1459) hydrogen bonds : angle 4.04970 ( 4254) covalent geometry : bond 0.00278 (25126) covalent geometry : angle 0.51077 (34072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 2.706 Fit side-chains revert: symmetry clash REVERT: A 1417 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.4902 (tpp) REVERT: A 1602 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 1649 LYS cc_start: 0.8171 (mttt) cc_final: 0.7828 (ttmm) REVERT: A 1914 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 2060 ARG cc_start: 0.7950 (ptt90) cc_final: 0.7379 (mpt90) REVERT: A 2169 GLN cc_start: 0.7050 (tp40) cc_final: 0.6649 (mm-40) REVERT: A 2308 ASP cc_start: 0.6244 (m-30) cc_final: 0.5914 (m-30) REVERT: A 2444 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: A 2510 MET cc_start: 0.7496 (mmm) cc_final: 0.6789 (mmt) REVERT: A 2522 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7498 (t) REVERT: A 2712 CYS cc_start: 0.8371 (m) cc_final: 0.7861 (p) REVERT: A 2902 GLU cc_start: 0.6663 (mp0) cc_final: 0.6359 (mp0) REVERT: A 3008 MET cc_start: 0.7893 (tpt) cc_final: 0.7637 (tpp) REVERT: A 3014 ASN cc_start: 0.7772 (t0) cc_final: 0.7023 (m-40) REVERT: A 3043 MET cc_start: 0.7731 (ptp) cc_final: 0.6732 (ppp) REVERT: A 3049 GLU cc_start: 0.7180 (tp30) cc_final: 0.6913 (mt-10) REVERT: A 3068 MET cc_start: 0.8231 (ptm) cc_final: 0.7270 (ptp) REVERT: A 3654 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6585 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7430 (tp40) cc_final: 0.7003 (mp10) REVERT: A 3968 GLN cc_start: 0.7810 (mt0) cc_final: 0.7504 (mm-40) REVERT: A 4108 GLN cc_start: 0.6286 (mm-40) cc_final: 0.5363 (mt0) REVERT: A 4128 MET cc_start: 0.8167 (mtt) cc_final: 0.7894 (mtm) REVERT: A 4271 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7872 (tmm-80) REVERT: A 4283 LYS cc_start: 0.8473 (mptt) cc_final: 0.8166 (mmtm) REVERT: A 4315 THR cc_start: 0.7840 (p) cc_final: 0.7566 (t) REVERT: A 4404 ASN cc_start: 0.4076 (m110) cc_final: 0.3617 (m110) outliers start: 29 outliers final: 18 residues processed: 288 average time/residue: 1.5012 time to fit residues: 497.3569 Evaluate side-chains 287 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 1.9990 chunk 174 optimal weight: 0.0970 chunk 191 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 299 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN ** A4466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121766 restraints weight = 38541.297| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.11 r_work: 0.3265 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25126 Z= 0.121 Angle : 0.511 14.745 34072 Z= 0.257 Chirality : 0.039 0.224 3817 Planarity : 0.004 0.074 4364 Dihedral : 6.428 112.714 3415 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.04 % Allowed : 12.94 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.15), residues: 3029 helix: 2.26 (0.12), residues: 1770 sheet: -0.58 (0.33), residues: 229 loop : 0.42 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.012 0.001 HIS A3200 PHE 0.019 0.001 PHE A3813 TYR 0.019 0.001 TYR A2748 ARG 0.016 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1459) hydrogen bonds : angle 4.03887 ( 4254) covalent geometry : bond 0.00280 (25126) covalent geometry : angle 0.51109 (34072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6058 Ramachandran restraints generated. 3029 Oldfield, 0 Emsley, 3029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 2.787 Fit side-chains revert: symmetry clash REVERT: A 1417 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.5003 (tpp) REVERT: A 1602 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 1649 LYS cc_start: 0.8180 (mttt) cc_final: 0.7837 (ttmm) REVERT: A 1914 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 2060 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7409 (mpt90) REVERT: A 2169 GLN cc_start: 0.7051 (tp40) cc_final: 0.6652 (mm-40) REVERT: A 2308 ASP cc_start: 0.6223 (m-30) cc_final: 0.5926 (m-30) REVERT: A 2444 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: A 2510 MET cc_start: 0.7503 (mmm) cc_final: 0.6835 (mmt) REVERT: A 2522 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7516 (t) REVERT: A 2593 LEU cc_start: 0.8151 (mt) cc_final: 0.7940 (mp) REVERT: A 2712 CYS cc_start: 0.8386 (m) cc_final: 0.7852 (p) REVERT: A 2885 ASP cc_start: 0.7526 (t0) cc_final: 0.7298 (t0) REVERT: A 2902 GLU cc_start: 0.6672 (mp0) cc_final: 0.6369 (mp0) REVERT: A 3008 MET cc_start: 0.7903 (tpt) cc_final: 0.7690 (tpp) REVERT: A 3014 ASN cc_start: 0.7796 (t0) cc_final: 0.7074 (m-40) REVERT: A 3043 MET cc_start: 0.7715 (ptp) cc_final: 0.6739 (ppp) REVERT: A 3049 GLU cc_start: 0.7195 (tp30) cc_final: 0.6930 (mt-10) REVERT: A 3068 MET cc_start: 0.8254 (ptm) cc_final: 0.7302 (ptp) REVERT: A 3654 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6576 (ptm-80) REVERT: A 3792 GLN cc_start: 0.7460 (tp40) cc_final: 0.7035 (mp10) REVERT: A 3968 GLN cc_start: 0.7844 (mt0) cc_final: 0.7540 (mm-40) REVERT: A 4108 GLN cc_start: 0.6324 (mm-40) cc_final: 0.5385 (mt0) REVERT: A 4128 MET cc_start: 0.8187 (mtt) cc_final: 0.7919 (mtm) REVERT: A 4271 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7908 (tmm-80) REVERT: A 4283 LYS cc_start: 0.8503 (mptt) cc_final: 0.8192 (mmtm) REVERT: A 4315 THR cc_start: 0.7842 (p) cc_final: 0.7578 (t) REVERT: A 4404 ASN cc_start: 0.4078 (m110) cc_final: 0.3616 (m110) outliers start: 27 outliers final: 18 residues processed: 283 average time/residue: 1.4932 time to fit residues: 486.3674 Evaluate side-chains 288 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2505 ASP Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2793 ILE Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3654 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3834 ASP Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4236 ASP Chi-restraints excluded: chain A residue 4518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 302 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 172 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 300 optimal weight: 0.1980 chunk 177 optimal weight: 2.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN ** A3820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123479 restraints weight = 33416.764| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.17 r_work: 0.3295 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25126 Z= 0.107 Angle : 0.496 14.235 34072 Z= 0.251 Chirality : 0.038 0.246 3817 Planarity : 0.004 0.076 4364 Dihedral : 6.264 111.970 3415 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 0.89 % Allowed : 13.24 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.16), residues: 3029 helix: 2.35 (0.12), residues: 1768 sheet: -0.63 (0.32), residues: 239 loop : 0.46 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.013 0.001 HIS A3200 PHE 0.017 0.001 PHE A3813 TYR 0.017 0.001 TYR A2748 ARG 0.017 0.000 ARG A2927 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1459) hydrogen bonds : angle 3.96557 ( 4254) covalent geometry : bond 0.00237 (25126) covalent geometry : angle 0.49613 (34072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20932.25 seconds wall clock time: 359 minutes 50.72 seconds (21590.72 seconds total)