Starting phenix.real_space_refine on Thu Jun 19 11:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmt_44710/06_2025/9bmt_44710.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 111 5.16 5 C 13892 2.51 5 N 3777 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.04, per 1000 atoms: 0.55 Number of scatterers: 21867 At special positions: 0 Unit cell: (148.493, 160.867, 115.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4078 8.00 N 3777 7.00 C 13892 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: 5.60 Conformation dependent library (CDL) restraints added in 2.7 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 18 sheets defined 61.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.778A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1649 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1796 Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 removed outlier: 3.674A pdb=" N VAL A1916 " --> pdb=" O LYS A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.696A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.550A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2131 Processing helix chain 'A' and resid 2133 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: 4.292A 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 removed outlier: 4.155A pdb=" N LEU A2237 " --> pdb=" O ALA A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.648A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2318 removed outlier: 3.534A pdb=" N SER A2317 " --> pdb=" O ASN A2314 " (cutoff:3.500A) 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 removed outlier: 3.780A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2423 Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.545A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.621A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) 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 2548 through 2552 Processing helix chain 'A' and resid 2558 through 2562 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.757A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2601 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.124A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2731 removed outlier: 4.269A pdb=" N HIS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A2731 " --> pdb=" O PHE A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 5.210A 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: 3.775A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2984 removed outlier: 3.511A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.171A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3061 removed outlier: 3.603A pdb=" N LEU A3050 " --> pdb=" O SER A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 removed outlier: 3.692A pdb=" N ARG A3088 " --> pdb=" O ALA A3084 " (cutoff:3.500A) 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 3220 removed outlier: 3.564A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A3196 " --> pdb=" O SER A3192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 4.799A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.965A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3737 removed outlier: 3.909A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3737 through 3755 Processing helix chain 'A' and resid 3766 through 3791 Processing helix chain 'A' and resid 3793 through 3818 removed outlier: 3.703A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.731A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 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: 6.132A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.512A pdb=" N LYS A3950 " --> pdb=" O ASP A3946 " (cutoff:3.500A) Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.697A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.119A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.982A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 4.100A 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: 3.570A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.751A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.312A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.681A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.745A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.673A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.330A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4209 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.691A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4407 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 3.748A 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 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 8.264A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.745A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.672A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 removed outlier: 3.562A pdb=" N MET A1861 " --> pdb=" O ALA A1864 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 5.955A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2219 through 2220 removed outlier: 6.786A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A2250 " --> pdb=" O ARG A2298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2222 through 2223 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 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: 5.839A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.839A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.241A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.245A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.321A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.079A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.951A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1254 hydrogen bonds defined for protein. 3660 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: 11.87 Time building geometry restraints manager: 6.48 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: 7210 1.34 - 1.46: 4690 1.46 - 1.58: 10244 1.58 - 1.70: 11 1.70 - 1.81: 185 Bond restraints: 22340 Sorted by residual: bond pdb=" CB GLU A3624 " pdb=" CG GLU A3624 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CG1 ILE A2049 " pdb=" CD1 ILE A2049 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG LEU A1879 " pdb=" CD1 LEU A1879 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB TRP A3489 " pdb=" CG TRP A3489 " ideal model delta sigma weight residual 1.498 1.464 0.034 3.10e-02 1.04e+03 1.19e+00 bond pdb=" CG1 ILE A1978 " pdb=" CD1 ILE A1978 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.16e+00 ... (remaining 22335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 29609 1.77 - 3.53: 591 3.53 - 5.30: 81 5.30 - 7.06: 22 7.06 - 8.83: 5 Bond angle restraints: 30308 Sorted by residual: angle pdb=" CA ARG A2118 " pdb=" CB ARG A2118 " pdb=" CG ARG A2118 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" N MET A3791 " pdb=" CA MET A3791 " pdb=" C MET A3791 " ideal model delta sigma weight residual 113.19 108.96 4.23 1.19e+00 7.06e-01 1.26e+01 angle pdb=" N PHE A3496 " pdb=" CA PHE A3496 " pdb=" CB PHE A3496 " ideal model delta sigma weight residual 110.20 105.23 4.97 1.49e+00 4.50e-01 1.11e+01 angle pdb=" C THR A4033 " pdb=" N GLU A4034 " pdb=" CA GLU A4034 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N VAL A2838 " pdb=" CA VAL A2838 " pdb=" C VAL A2838 " ideal model delta sigma weight residual 112.96 110.16 2.80 1.00e+00 1.00e+00 7.82e+00 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 12954 27.54 - 55.08: 507 55.08 - 82.62: 77 82.62 - 110.17: 2 110.17 - 137.71: 2 Dihedral angle restraints: 13542 sinusoidal: 5612 harmonic: 7930 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 77.70 -137.71 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 177.72 122.28 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" CA GLU A3195 " pdb=" C GLU A3195 " pdb=" N GLU A3196 " pdb=" CA GLU A3196 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 13539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2565 0.041 - 0.082: 617 0.082 - 0.124: 214 0.124 - 0.165: 15 0.165 - 0.206: 1 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CG LEU A2097 " pdb=" CB LEU A2097 " pdb=" CD1 LEU A2097 " pdb=" CD2 LEU A2097 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A1698 " pdb=" CA ILE A1698 " pdb=" CG1 ILE A1698 " pdb=" CG2 ILE A1698 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CG LEU A3020 " pdb=" CB LEU A3020 " pdb=" CD1 LEU A3020 " pdb=" CD2 LEU A3020 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 3409 not shown) Planarity restraints: 3883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A3496 " -0.029 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE A3496 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A3496 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A3496 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A3496 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A3496 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A3496 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2682 " -0.021 2.00e-02 2.50e+03 1.90e-02 6.32e+00 pdb=" CG PHE A2682 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A2682 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A2682 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A2682 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A2682 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A2682 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A3672 " -0.033 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO A3673 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A3673 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A3673 " -0.028 5.00e-02 4.00e+02 ... (remaining 3880 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 285 2.65 - 3.22: 21960 3.22 - 3.78: 36240 3.78 - 4.34: 47527 4.34 - 4.90: 76314 Nonbonded interactions: 182326 Sorted by model distance: nonbonded pdb=" O ILE A2253 " pdb=" OH TYR A2693 " model vdw 2.092 3.040 nonbonded pdb=" OG SER A4535 " pdb=" OE1 GLU A4537 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A2644 " pdb=" O GLY A2647 " model vdw 2.205 3.040 nonbonded pdb=" O GLY A3106 " pdb=" OG1 THR A3110 " model vdw 2.216 3.040 nonbonded pdb=" O VAL A4288 " pdb=" OG SER A4319 " model vdw 2.218 3.040 ... (remaining 182321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 53.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22340 Z= 0.137 Angle : 0.620 8.830 30308 Z= 0.324 Chirality : 0.040 0.206 3412 Planarity : 0.004 0.055 3883 Dihedral : 14.373 137.708 8390 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.16), residues: 2699 helix: 1.89 (0.13), residues: 1481 sheet: -0.61 (0.33), residues: 221 loop : 0.25 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2300 HIS 0.009 0.001 HIS A1921 PHE 0.055 0.002 PHE A3496 TYR 0.022 0.002 TYR A2881 ARG 0.013 0.001 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.13693 ( 1254) hydrogen bonds : angle 5.88093 ( 3660) covalent geometry : bond 0.00294 (22340) covalent geometry : angle 0.62011 (30308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7853 (pmm) cc_final: 0.7634 (pmm) REVERT: A 2284 LEU cc_start: 0.7836 (mt) cc_final: 0.7524 (mt) REVERT: A 2860 ASN cc_start: 0.7107 (p0) cc_final: 0.6879 (p0) REVERT: A 3532 TRP cc_start: 0.8526 (m-10) cc_final: 0.7899 (m-90) REVERT: A 4027 LEU cc_start: 0.7876 (mt) cc_final: 0.6462 (mp) outliers start: 1 outliers final: 1 residues processed: 342 average time/residue: 0.2997 time to fit residues: 167.6350 Evaluate side-chains 241 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3092 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1818 GLN A1856 GLN ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2252 HIS A2485 GLN A2932 HIS ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3197 GLN A3198 GLN A3584 ASN A4436 GLN A4526 GLN A4597 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.104371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079749 restraints weight = 71719.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082641 restraints weight = 39755.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083813 restraints weight = 22865.762| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22340 Z= 0.181 Angle : 0.629 7.434 30308 Z= 0.316 Chirality : 0.041 0.201 3412 Planarity : 0.004 0.051 3883 Dihedral : 6.843 148.161 3014 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.16 % Allowed : 8.60 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2699 helix: 1.77 (0.13), residues: 1514 sheet: -0.75 (0.33), residues: 216 loop : 0.31 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4105 HIS 0.009 0.001 HIS A1817 PHE 0.027 0.002 PHE A3187 TYR 0.030 0.002 TYR A1630 ARG 0.008 0.001 ARG A1943 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1254) hydrogen bonds : angle 5.01088 ( 3660) covalent geometry : bond 0.00405 (22340) covalent geometry : angle 0.62852 (30308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7967 (pmm) cc_final: 0.7634 (pmm) REVERT: A 1701 TRP cc_start: 0.8102 (p-90) cc_final: 0.7796 (p-90) REVERT: A 1756 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9072 (mp) REVERT: A 1850 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7527 (tp-100) REVERT: A 1960 PHE cc_start: 0.9092 (t80) cc_final: 0.8859 (t80) REVERT: A 2005 GLN cc_start: 0.6863 (mm110) cc_final: 0.6617 (mm110) REVERT: A 2012 MET cc_start: 0.8515 (tpp) cc_final: 0.7995 (tmm) REVERT: A 2205 GLU cc_start: 0.8964 (tp30) cc_final: 0.8756 (tp30) REVERT: A 2284 LEU cc_start: 0.8030 (mt) cc_final: 0.7629 (mt) REVERT: A 2373 MET cc_start: 0.7858 (mtm) cc_final: 0.7452 (mtm) REVERT: A 2449 LEU cc_start: 0.8309 (tp) cc_final: 0.7979 (tp) REVERT: A 2582 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8363 (t80) REVERT: A 2755 MET cc_start: 0.9272 (tpp) cc_final: 0.9054 (ttm) REVERT: A 3835 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9114 (mp) REVERT: A 4043 MET cc_start: 0.8435 (mtm) cc_final: 0.8111 (mtm) REVERT: A 4296 MET cc_start: 0.8723 (tmm) cc_final: 0.8454 (tmm) REVERT: A 4457 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7909 (pttt) outliers start: 28 outliers final: 13 residues processed: 280 average time/residue: 0.3015 time to fit residues: 140.6183 Evaluate side-chains 249 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2252 HIS Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4028 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 139 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 170 optimal weight: 0.3980 chunk 249 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1779 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2171 HIS A2252 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082840 restraints weight = 69152.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085128 restraints weight = 37500.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086614 restraints weight = 25900.423| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22340 Z= 0.146 Angle : 0.587 9.471 30308 Z= 0.290 Chirality : 0.040 0.227 3412 Planarity : 0.004 0.052 3883 Dihedral : 6.744 150.141 3014 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.12 % Allowed : 12.09 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2699 helix: 1.80 (0.13), residues: 1514 sheet: -0.93 (0.32), residues: 225 loop : 0.33 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2300 HIS 0.012 0.001 HIS A2252 PHE 0.019 0.002 PHE A2479 TYR 0.024 0.002 TYR A2693 ARG 0.003 0.000 ARG A3611 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 1254) hydrogen bonds : angle 4.74590 ( 3660) covalent geometry : bond 0.00328 (22340) covalent geometry : angle 0.58683 (30308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7964 (pmm) cc_final: 0.7618 (pmm) REVERT: A 1756 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9122 (mp) REVERT: A 1850 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7619 (tp-100) REVERT: A 1974 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 2005 GLN cc_start: 0.6820 (mm110) cc_final: 0.6547 (mm110) REVERT: A 2205 GLU cc_start: 0.8933 (tp30) cc_final: 0.8678 (tp30) REVERT: A 2306 ASP cc_start: 0.5489 (t70) cc_final: 0.5285 (t0) REVERT: A 2373 MET cc_start: 0.7819 (mtm) cc_final: 0.7467 (mtm) REVERT: A 2449 LEU cc_start: 0.8328 (tp) cc_final: 0.8046 (tp) REVERT: A 2994 MET cc_start: 0.7653 (tpt) cc_final: 0.7344 (tpt) REVERT: A 3187 PHE cc_start: 0.8461 (t80) cc_final: 0.8061 (t80) REVERT: A 3496 PHE cc_start: 0.3647 (t80) cc_final: 0.3203 (t80) REVERT: A 3835 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9076 (mp) REVERT: A 4043 MET cc_start: 0.8476 (mtm) cc_final: 0.8131 (mtm) REVERT: A 4339 MET cc_start: 0.9313 (tmm) cc_final: 0.8795 (tmm) outliers start: 27 outliers final: 19 residues processed: 280 average time/residue: 0.3043 time to fit residues: 141.0755 Evaluate side-chains 259 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4521 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 53 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 260 optimal weight: 0.2980 chunk 39 optimal weight: 0.0570 chunk 125 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 4 optimal weight: 0.0470 chunk 218 optimal weight: 0.9980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1817 HIS A1818 GLN A1881 GLN A1974 GLN A2577 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN A3499 GLN A3636 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.105544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079444 restraints weight = 71817.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081828 restraints weight = 38298.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083468 restraints weight = 26250.098| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22340 Z= 0.111 Angle : 0.569 8.389 30308 Z= 0.280 Chirality : 0.040 0.204 3412 Planarity : 0.004 0.053 3883 Dihedral : 6.597 150.844 3014 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.62 % Allowed : 12.84 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.17), residues: 2699 helix: 1.87 (0.13), residues: 1519 sheet: -0.84 (0.32), residues: 250 loop : 0.32 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2300 HIS 0.011 0.001 HIS A1817 PHE 0.018 0.001 PHE A1960 TYR 0.024 0.001 TYR A2693 ARG 0.005 0.000 ARG A2977 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 1254) hydrogen bonds : angle 4.55603 ( 3660) covalent geometry : bond 0.00240 (22340) covalent geometry : angle 0.56926 (30308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7889 (pmm) cc_final: 0.7543 (pmm) REVERT: A 1701 TRP cc_start: 0.8029 (p-90) cc_final: 0.7683 (p-90) REVERT: A 1727 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 1733 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7372 (tp) REVERT: A 1756 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9062 (mp) REVERT: A 1945 PHE cc_start: 0.9078 (t80) cc_final: 0.8865 (t80) REVERT: A 1960 PHE cc_start: 0.9120 (t80) cc_final: 0.8809 (t80) REVERT: A 1967 MET cc_start: 0.8879 (mmm) cc_final: 0.8515 (mmm) REVERT: A 1974 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: A 2300 TRP cc_start: 0.8091 (m-10) cc_final: 0.7689 (m-10) REVERT: A 2306 ASP cc_start: 0.5375 (t70) cc_final: 0.5170 (t0) REVERT: A 2373 MET cc_start: 0.7799 (mtm) cc_final: 0.7526 (mtm) REVERT: A 2449 LEU cc_start: 0.8250 (tp) cc_final: 0.7938 (tp) REVERT: A 2799 MET cc_start: 0.8551 (ttm) cc_final: 0.8155 (ttm) REVERT: A 2994 MET cc_start: 0.7697 (tpt) cc_final: 0.7309 (tpt) REVERT: A 3054 PHE cc_start: 0.8981 (t80) cc_final: 0.8762 (t80) REVERT: A 3835 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9059 (mp) REVERT: A 3933 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9009 (mp0) REVERT: A 4043 MET cc_start: 0.8546 (mtm) cc_final: 0.8137 (mtm) REVERT: A 4211 ASP cc_start: 0.8966 (p0) cc_final: 0.8382 (p0) REVERT: A 4339 MET cc_start: 0.9274 (tmm) cc_final: 0.8758 (tmm) REVERT: A 4380 LEU cc_start: 0.9103 (tp) cc_final: 0.8833 (tt) outliers start: 39 outliers final: 14 residues processed: 310 average time/residue: 0.3224 time to fit residues: 165.4070 Evaluate side-chains 262 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3045 ASP Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 GLN A2005 GLN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A4325 ASN A4386 ASN A4397 HIS A4526 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078468 restraints weight = 71470.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080683 restraints weight = 39170.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082098 restraints weight = 27251.217| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22340 Z= 0.256 Angle : 0.672 10.204 30308 Z= 0.335 Chirality : 0.042 0.242 3412 Planarity : 0.004 0.058 3883 Dihedral : 6.807 145.427 3014 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 14.04 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.16), residues: 2699 helix: 1.69 (0.13), residues: 1520 sheet: -0.76 (0.33), residues: 240 loop : 0.18 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A4222 HIS 0.020 0.002 HIS A2085 PHE 0.025 0.002 PHE A3496 TYR 0.029 0.002 TYR A3176 ARG 0.004 0.001 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1254) hydrogen bonds : angle 4.71080 ( 3660) covalent geometry : bond 0.00572 (22340) covalent geometry : angle 0.67154 (30308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8021 (pmm) cc_final: 0.7687 (pmm) REVERT: A 1756 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 1850 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7709 (tp-100) REVERT: A 1960 PHE cc_start: 0.9156 (t80) cc_final: 0.8871 (t80) REVERT: A 1967 MET cc_start: 0.8812 (mmm) cc_final: 0.8529 (mmm) REVERT: A 2306 ASP cc_start: 0.5446 (t70) cc_final: 0.5234 (t0) REVERT: A 2324 LEU cc_start: 0.8303 (pt) cc_final: 0.7758 (tt) REVERT: A 2342 MET cc_start: 0.7806 (mtm) cc_final: 0.7018 (mtt) REVERT: A 2373 MET cc_start: 0.8228 (mtm) cc_final: 0.7923 (mtm) REVERT: A 2737 ASP cc_start: 0.8788 (t0) cc_final: 0.8534 (m-30) REVERT: A 2755 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8751 (ttp) REVERT: A 2897 LEU cc_start: 0.9177 (tp) cc_final: 0.8824 (tp) REVERT: A 2994 MET cc_start: 0.7762 (tpt) cc_final: 0.7360 (tpt) REVERT: A 3054 PHE cc_start: 0.9050 (t80) cc_final: 0.8797 (t80) REVERT: A 3523 GLN cc_start: 0.8826 (mp10) cc_final: 0.8566 (mp10) REVERT: A 3835 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9128 (mp) REVERT: A 4043 MET cc_start: 0.8602 (mtm) cc_final: 0.8267 (mtm) REVERT: A 4339 MET cc_start: 0.9325 (tmm) cc_final: 0.8705 (tmm) REVERT: A 4457 LYS cc_start: 0.8378 (pttt) cc_final: 0.8071 (pttm) outliers start: 51 outliers final: 33 residues processed: 274 average time/residue: 0.3450 time to fit residues: 162.6899 Evaluate side-chains 270 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2228 SER Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4182 LEU Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 6 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080903 restraints weight = 70116.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083189 restraints weight = 37865.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084693 restraints weight = 26084.123| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.127 Angle : 0.584 9.811 30308 Z= 0.287 Chirality : 0.040 0.211 3412 Planarity : 0.004 0.053 3883 Dihedral : 6.629 147.946 3014 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.74 % Allowed : 15.62 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.17), residues: 2699 helix: 1.85 (0.13), residues: 1521 sheet: -0.67 (0.34), residues: 237 loop : 0.21 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2300 HIS 0.006 0.001 HIS A1817 PHE 0.050 0.002 PHE A2635 TYR 0.021 0.002 TYR A3519 ARG 0.004 0.000 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 1254) hydrogen bonds : angle 4.52293 ( 3660) covalent geometry : bond 0.00286 (22340) covalent geometry : angle 0.58383 (30308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7979 (pmm) cc_final: 0.7631 (pmm) REVERT: A 1701 TRP cc_start: 0.7961 (p-90) cc_final: 0.7692 (p-90) REVERT: A 1756 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9090 (mp) REVERT: A 1960 PHE cc_start: 0.9149 (t80) cc_final: 0.8948 (t80) REVERT: A 2300 TRP cc_start: 0.8310 (m-10) cc_final: 0.7773 (m-10) REVERT: A 2306 ASP cc_start: 0.5342 (t70) cc_final: 0.5134 (t0) REVERT: A 2324 LEU cc_start: 0.8330 (pt) cc_final: 0.7764 (tt) REVERT: A 2373 MET cc_start: 0.8130 (mtm) cc_final: 0.7830 (mtm) REVERT: A 2737 ASP cc_start: 0.8799 (t0) cc_final: 0.8543 (m-30) REVERT: A 2755 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8424 (tpp) REVERT: A 2773 MET cc_start: 0.8822 (mtm) cc_final: 0.8399 (mtm) REVERT: A 2851 ASP cc_start: 0.8249 (t70) cc_final: 0.7999 (t0) REVERT: A 2994 MET cc_start: 0.7743 (tpt) cc_final: 0.7328 (tpt) REVERT: A 3054 PHE cc_start: 0.9002 (t80) cc_final: 0.8723 (t80) REVERT: A 3187 PHE cc_start: 0.8483 (t80) cc_final: 0.8112 (t80) REVERT: A 3835 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9096 (mp) REVERT: A 3873 ARG cc_start: 0.8797 (mmt180) cc_final: 0.8453 (mmt180) REVERT: A 3933 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8940 (mp0) REVERT: A 4043 MET cc_start: 0.8564 (mtm) cc_final: 0.8213 (mtm) REVERT: A 4339 MET cc_start: 0.9311 (tmm) cc_final: 0.8781 (tmm) outliers start: 42 outliers final: 27 residues processed: 282 average time/residue: 0.3133 time to fit residues: 148.8320 Evaluate side-chains 261 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4338 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.102434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077268 restraints weight = 71872.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079491 restraints weight = 39331.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080934 restraints weight = 27270.022| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22340 Z= 0.246 Angle : 0.683 11.294 30308 Z= 0.340 Chirality : 0.042 0.242 3412 Planarity : 0.004 0.054 3883 Dihedral : 6.833 142.919 3014 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.37 % Allowed : 16.33 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.16), residues: 2699 helix: 1.67 (0.13), residues: 1520 sheet: -0.86 (0.33), residues: 242 loop : 0.10 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2300 HIS 0.008 0.002 HIS A1817 PHE 0.043 0.002 PHE A2635 TYR 0.021 0.002 TYR A3519 ARG 0.008 0.001 ARG A2037 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 1254) hydrogen bonds : angle 4.72840 ( 3660) covalent geometry : bond 0.00551 (22340) covalent geometry : angle 0.68271 (30308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8170 (pmm) cc_final: 0.7757 (pmm) REVERT: A 1756 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9111 (mp) REVERT: A 1967 MET cc_start: 0.8700 (mmm) cc_final: 0.8312 (mmm) REVERT: A 2300 TRP cc_start: 0.8471 (m-10) cc_final: 0.7814 (m-10) REVERT: A 2324 LEU cc_start: 0.8352 (pt) cc_final: 0.7762 (tt) REVERT: A 2373 MET cc_start: 0.8360 (mtm) cc_final: 0.8020 (mtm) REVERT: A 2499 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 2731 VAL cc_start: 0.9199 (t) cc_final: 0.8980 (m) REVERT: A 2755 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8530 (tpp) REVERT: A 2917 ASP cc_start: 0.8921 (t0) cc_final: 0.8449 (t0) REVERT: A 2994 MET cc_start: 0.7811 (tpt) cc_final: 0.7365 (tpt) REVERT: A 3054 PHE cc_start: 0.9068 (t80) cc_final: 0.8804 (t80) REVERT: A 3187 PHE cc_start: 0.8604 (t80) cc_final: 0.8306 (t80) REVERT: A 3835 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9136 (mp) REVERT: A 3873 ARG cc_start: 0.8811 (mmt180) cc_final: 0.8585 (mmm-85) REVERT: A 3933 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8786 (mp0) REVERT: A 4043 MET cc_start: 0.8569 (mtm) cc_final: 0.8216 (mtm) REVERT: A 4296 MET cc_start: 0.8940 (tpt) cc_final: 0.8661 (tpp) REVERT: A 4339 MET cc_start: 0.9360 (tmm) cc_final: 0.8772 (tmm) outliers start: 57 outliers final: 43 residues processed: 279 average time/residue: 0.3030 time to fit residues: 141.4176 Evaluate side-chains 272 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2005 GLN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2635 PHE Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN A2171 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4589 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079487 restraints weight = 70948.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081763 restraints weight = 38387.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083263 restraints weight = 26586.550| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22340 Z= 0.142 Angle : 0.621 10.317 30308 Z= 0.303 Chirality : 0.040 0.221 3412 Planarity : 0.004 0.054 3883 Dihedral : 6.663 144.772 3014 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 17.32 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.17), residues: 2699 helix: 1.84 (0.13), residues: 1513 sheet: -0.93 (0.34), residues: 225 loop : 0.17 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2300 HIS 0.006 0.001 HIS A1921 PHE 0.046 0.002 PHE A2635 TYR 0.019 0.001 TYR A3519 ARG 0.005 0.000 ARG A3206 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1254) hydrogen bonds : angle 4.51476 ( 3660) covalent geometry : bond 0.00323 (22340) covalent geometry : angle 0.62145 (30308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8164 (pmm) cc_final: 0.7730 (pmm) REVERT: A 1756 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9064 (mp) REVERT: A 2300 TRP cc_start: 0.8394 (m-10) cc_final: 0.7814 (m-10) REVERT: A 2324 LEU cc_start: 0.8333 (pt) cc_final: 0.7728 (tt) REVERT: A 2361 MET cc_start: 0.8343 (ttp) cc_final: 0.7816 (ttp) REVERT: A 2373 MET cc_start: 0.8179 (mtm) cc_final: 0.7856 (mtm) REVERT: A 2499 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 2731 VAL cc_start: 0.9138 (t) cc_final: 0.8920 (m) REVERT: A 2755 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: A 2917 ASP cc_start: 0.8864 (t0) cc_final: 0.8389 (t0) REVERT: A 2994 MET cc_start: 0.7828 (tpt) cc_final: 0.7360 (tpt) REVERT: A 3054 PHE cc_start: 0.8996 (t80) cc_final: 0.8700 (t80) REVERT: A 3579 MET cc_start: 0.8335 (mtp) cc_final: 0.8033 (mtp) REVERT: A 3835 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9121 (mp) REVERT: A 3873 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8532 (mmt180) REVERT: A 3933 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8912 (mp0) REVERT: A 4043 MET cc_start: 0.8540 (mtm) cc_final: 0.8173 (mtm) REVERT: A 4296 MET cc_start: 0.8760 (tpt) cc_final: 0.8398 (tpp) REVERT: A 4339 MET cc_start: 0.9344 (tmm) cc_final: 0.8870 (tmm) outliers start: 47 outliers final: 37 residues processed: 272 average time/residue: 0.3168 time to fit residues: 143.5525 Evaluate side-chains 265 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2751 PHE Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2851 ASP Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4182 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2171 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079467 restraints weight = 70916.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081719 restraints weight = 38467.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083222 restraints weight = 26621.496| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22340 Z= 0.150 Angle : 0.642 15.842 30308 Z= 0.311 Chirality : 0.041 0.217 3412 Planarity : 0.004 0.048 3883 Dihedral : 6.644 143.503 3014 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.74 % Allowed : 17.95 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2699 helix: 1.84 (0.13), residues: 1516 sheet: -0.95 (0.35), residues: 225 loop : 0.19 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1701 HIS 0.006 0.001 HIS A1921 PHE 0.019 0.001 PHE A1945 TYR 0.017 0.001 TYR A3519 ARG 0.007 0.000 ARG A2037 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1254) hydrogen bonds : angle 4.53033 ( 3660) covalent geometry : bond 0.00343 (22340) covalent geometry : angle 0.64161 (30308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8200 (pmm) cc_final: 0.7754 (pmm) REVERT: A 1756 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9075 (mp) REVERT: A 2300 TRP cc_start: 0.8412 (m-10) cc_final: 0.7875 (m-10) REVERT: A 2324 LEU cc_start: 0.8333 (pt) cc_final: 0.7719 (tt) REVERT: A 2361 MET cc_start: 0.8320 (ttp) cc_final: 0.7727 (ttp) REVERT: A 2373 MET cc_start: 0.8218 (mtm) cc_final: 0.7930 (mtm) REVERT: A 2481 MET cc_start: 0.5180 (ppp) cc_final: 0.4973 (ptp) REVERT: A 2731 VAL cc_start: 0.9135 (t) cc_final: 0.8910 (m) REVERT: A 2755 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8578 (tpp) REVERT: A 2917 ASP cc_start: 0.8891 (t0) cc_final: 0.8408 (t0) REVERT: A 2994 MET cc_start: 0.7756 (tpt) cc_final: 0.7270 (tpt) REVERT: A 3054 PHE cc_start: 0.9035 (t80) cc_final: 0.8749 (t80) REVERT: A 3130 TYR cc_start: 0.8118 (t80) cc_final: 0.7822 (t80) REVERT: A 3502 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 3579 MET cc_start: 0.8386 (mtp) cc_final: 0.8100 (mtp) REVERT: A 3835 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9126 (mp) REVERT: A 3873 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8370 (mmt180) REVERT: A 3933 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8918 (mp0) REVERT: A 4043 MET cc_start: 0.8478 (mtm) cc_final: 0.8092 (mtm) REVERT: A 4296 MET cc_start: 0.8666 (tpt) cc_final: 0.8274 (tpp) REVERT: A 4339 MET cc_start: 0.9353 (tmm) cc_final: 0.8834 (tmm) outliers start: 42 outliers final: 36 residues processed: 260 average time/residue: 0.3069 time to fit residues: 132.4261 Evaluate side-chains 264 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2851 ASP Chi-restraints excluded: chain A residue 2956 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3502 THR Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4182 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 104 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089795 restraints weight = 71934.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092280 restraints weight = 37441.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093983 restraints weight = 25408.392| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.140 Angle : 0.638 13.801 30308 Z= 0.310 Chirality : 0.041 0.214 3412 Planarity : 0.004 0.048 3883 Dihedral : 6.592 143.856 3014 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.66 % Allowed : 18.24 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2699 helix: 1.83 (0.13), residues: 1521 sheet: -0.93 (0.35), residues: 225 loop : 0.18 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1701 HIS 0.006 0.001 HIS A1921 PHE 0.015 0.001 PHE A4260 TYR 0.017 0.001 TYR A2748 ARG 0.007 0.000 ARG A2037 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1254) hydrogen bonds : angle 4.49833 ( 3660) covalent geometry : bond 0.00322 (22340) covalent geometry : angle 0.63754 (30308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8192 (pmm) cc_final: 0.7788 (pmm) REVERT: A 1756 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9082 (mp) REVERT: A 2145 MET cc_start: 0.8810 (mmm) cc_final: 0.8323 (mmm) REVERT: A 2300 TRP cc_start: 0.8386 (m-10) cc_final: 0.7943 (m-10) REVERT: A 2324 LEU cc_start: 0.8322 (pt) cc_final: 0.7742 (tt) REVERT: A 2361 MET cc_start: 0.8364 (ttp) cc_final: 0.7793 (ttp) REVERT: A 2373 MET cc_start: 0.8134 (mtm) cc_final: 0.7854 (mtm) REVERT: A 2449 LEU cc_start: 0.8354 (tp) cc_final: 0.7954 (tp) REVERT: A 2731 VAL cc_start: 0.9128 (t) cc_final: 0.8921 (m) REVERT: A 2755 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8553 (tpp) REVERT: A 2917 ASP cc_start: 0.8836 (t0) cc_final: 0.8348 (t0) REVERT: A 2994 MET cc_start: 0.7742 (tpt) cc_final: 0.7272 (tpt) REVERT: A 3008 MET cc_start: 0.9245 (mmm) cc_final: 0.8943 (mpp) REVERT: A 3054 PHE cc_start: 0.9027 (t80) cc_final: 0.8752 (t80) REVERT: A 3130 TYR cc_start: 0.8081 (t80) cc_final: 0.7869 (t80) REVERT: A 3835 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9181 (mp) REVERT: A 3873 ARG cc_start: 0.8745 (mmt180) cc_final: 0.8286 (mmt180) REVERT: A 3933 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: A 4043 MET cc_start: 0.8474 (mtm) cc_final: 0.8085 (mtm) REVERT: A 4296 MET cc_start: 0.8510 (tpt) cc_final: 0.8139 (tpp) REVERT: A 4339 MET cc_start: 0.9309 (tmm) cc_final: 0.8811 (tmm) outliers start: 40 outliers final: 33 residues processed: 262 average time/residue: 0.3077 time to fit residues: 133.9438 Evaluate side-chains 260 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2093 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2182 LEU Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2751 PHE Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2851 ASP Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3619 PHE Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4182 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 211 optimal weight: 0.0980 chunk 48 optimal weight: 7.9990 chunk 265 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 252 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.106770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081500 restraints weight = 70624.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083947 restraints weight = 36742.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085574 restraints weight = 24768.889| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22340 Z= 0.118 Angle : 0.635 13.634 30308 Z= 0.306 Chirality : 0.040 0.200 3412 Planarity : 0.004 0.048 3883 Dihedral : 6.480 144.657 3014 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 18.94 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.17), residues: 2699 helix: 1.92 (0.13), residues: 1515 sheet: -0.86 (0.36), residues: 222 loop : 0.25 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.006 0.001 HIS A1921 PHE 0.041 0.001 PHE A1945 TYR 0.017 0.001 TYR A3183 ARG 0.006 0.000 ARG A2037 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1254) hydrogen bonds : angle 4.42442 ( 3660) covalent geometry : bond 0.00266 (22340) covalent geometry : angle 0.63549 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.97 seconds wall clock time: 131 minutes 24.52 seconds (7884.52 seconds total)