Starting phenix.real_space_refine on Fri Sep 19 02:33:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmt_44710/09_2025/9bmt_44710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmt_44710/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bmt_44710/09_2025/9bmt_44710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmt_44710/09_2025/9bmt_44710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bmt_44710/09_2025/9bmt_44710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmt_44710/09_2025/9bmt_44710.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.77, per 1000 atoms: 0.22 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: 1.70 Conformation dependent library (CDL) restraints added in 973.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.11 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: 6.29 Time building geometry restraints manager: 2.35 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: 2.720 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG A2844 TYR 0.022 0.002 TYR A2881 PHE 0.055 0.002 PHE A3496 TRP 0.021 0.001 TRP A2300 HIS 0.009 0.001 HIS A1921 Details of bonding type rmsd covalent geometry : bond 0.00294 (22340) covalent geometry : angle 0.62011 (30308) hydrogen bonds : bond 0.13693 ( 1254) hydrogen bonds : angle 5.88093 ( 3660) *********************** 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 : 0.844 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: 0.1315 time to fit residues: 73.7042 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 : 0.826 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 A3197 GLN A3198 GLN A3535 HIS A3584 ASN A4326 ASN A4436 GLN A4526 GLN A4597 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.104258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.079572 restraints weight = 72027.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082543 restraints weight = 40119.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083799 restraints weight = 22738.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083842 restraints weight = 20227.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083760 restraints weight = 17592.623| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22340 Z= 0.186 Angle : 0.636 7.455 30308 Z= 0.319 Chirality : 0.041 0.182 3412 Planarity : 0.004 0.051 3883 Dihedral : 6.848 147.840 3014 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 8.52 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 2699 helix: 1.78 (0.13), residues: 1513 sheet: -0.74 (0.33), residues: 216 loop : 0.30 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1943 TYR 0.028 0.002 TYR A2693 PHE 0.027 0.002 PHE A3187 TRP 0.013 0.001 TRP A4105 HIS 0.009 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00422 (22340) covalent geometry : angle 0.63571 (30308) hydrogen bonds : bond 0.04309 ( 1254) hydrogen bonds : angle 5.02492 ( 3660) *********************** 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 290 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7963 (pmm) cc_final: 0.7631 (pmm) REVERT: A 1756 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9080 (mp) REVERT: A 1850 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7531 (tp-100) REVERT: A 2005 GLN cc_start: 0.6802 (mm110) cc_final: 0.6561 (mm110) REVERT: A 2205 GLU cc_start: 0.8963 (tp30) cc_final: 0.8751 (tp30) REVERT: A 2284 LEU cc_start: 0.8032 (mt) cc_final: 0.7643 (mt) REVERT: A 2373 MET cc_start: 0.7777 (mtm) cc_final: 0.7367 (mtm) REVERT: A 2449 LEU cc_start: 0.8278 (tp) cc_final: 0.7989 (tp) REVERT: A 2582 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (t80) REVERT: A 2755 MET cc_start: 0.9275 (tpp) cc_final: 0.9035 (ttm) REVERT: A 3835 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9115 (mp) REVERT: A 4043 MET cc_start: 0.8444 (mtm) cc_final: 0.8116 (mtm) REVERT: A 4296 MET cc_start: 0.8722 (tmm) cc_final: 0.8458 (tmm) REVERT: A 4457 LYS cc_start: 0.8215 (ptpp) cc_final: 0.7921 (pttt) outliers start: 29 outliers final: 13 residues processed: 278 average time/residue: 0.1254 time to fit residues: 58.1188 Evaluate side-chains 247 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A1974 GLN A2171 HIS A2252 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3636 GLN A4526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083135 restraints weight = 70773.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085482 restraints weight = 38080.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087023 restraints weight = 26123.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088018 restraints weight = 20700.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088505 restraints weight = 18015.548| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1583 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= 0.128 Angle : 0.581 9.442 30308 Z= 0.287 Chirality : 0.040 0.224 3412 Planarity : 0.004 0.052 3883 Dihedral : 6.728 150.351 3014 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.16 % Allowed : 11.84 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 2699 helix: 1.80 (0.13), residues: 1514 sheet: -0.96 (0.32), residues: 227 loop : 0.35 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3611 TYR 0.021 0.001 TYR A2693 PHE 0.021 0.002 PHE A1727 TRP 0.019 0.001 TRP A2300 HIS 0.012 0.001 HIS A2252 Details of bonding type rmsd covalent geometry : bond 0.00285 (22340) covalent geometry : angle 0.58119 (30308) hydrogen bonds : bond 0.03886 ( 1254) hydrogen bonds : angle 4.73370 ( 3660) *********************** 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 296 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7960 (pmm) cc_final: 0.7599 (pmm) REVERT: A 1756 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 1850 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7583 (tp-100) REVERT: A 1929 VAL cc_start: 0.9280 (m) cc_final: 0.9067 (t) REVERT: A 2005 GLN cc_start: 0.6771 (mm110) cc_final: 0.6497 (mm110) REVERT: A 2324 LEU cc_start: 0.8168 (pp) cc_final: 0.7921 (tt) REVERT: A 2373 MET cc_start: 0.7731 (mtm) cc_final: 0.7361 (mtm) REVERT: A 2449 LEU cc_start: 0.8280 (tp) cc_final: 0.7965 (tp) REVERT: A 2686 MET cc_start: 0.8195 (ptm) cc_final: 0.7990 (ptm) REVERT: A 2799 MET cc_start: 0.8530 (ttm) cc_final: 0.8100 (ttm) REVERT: A 2994 MET cc_start: 0.7607 (tpt) cc_final: 0.7221 (tpt) REVERT: A 3054 PHE cc_start: 0.8991 (t80) cc_final: 0.8719 (t80) REVERT: A 3066 PHE cc_start: 0.8463 (m-80) cc_final: 0.8220 (m-10) REVERT: A 3187 PHE cc_start: 0.8502 (t80) cc_final: 0.8074 (t80) REVERT: A 3496 PHE cc_start: 0.3502 (t80) cc_final: 0.3129 (t80) REVERT: A 3835 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9063 (mp) REVERT: A 4043 MET cc_start: 0.8447 (mtm) cc_final: 0.8103 (mtm) REVERT: A 4211 ASP cc_start: 0.8924 (p0) cc_final: 0.8400 (p0) REVERT: A 4339 MET cc_start: 0.9295 (tmm) cc_final: 0.8789 (tmm) outliers start: 28 outliers final: 17 residues processed: 283 average time/residue: 0.1218 time to fit residues: 57.1120 Evaluate side-chains 260 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 1948 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 3 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ** A1921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2577 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN A4526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.104059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077886 restraints weight = 71767.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080198 restraints weight = 38390.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.081738 restraints weight = 26456.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082411 restraints weight = 21229.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083241 restraints weight = 18963.198| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22340 Z= 0.132 Angle : 0.569 8.379 30308 Z= 0.282 Chirality : 0.040 0.214 3412 Planarity : 0.004 0.056 3883 Dihedral : 6.651 149.498 3014 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 12.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.17), residues: 2699 helix: 1.86 (0.13), residues: 1521 sheet: -0.83 (0.33), residues: 244 loop : 0.29 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2977 TYR 0.025 0.001 TYR A2693 PHE 0.033 0.001 PHE A1945 TRP 0.014 0.001 TRP A2300 HIS 0.016 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00294 (22340) covalent geometry : angle 0.56894 (30308) hydrogen bonds : bond 0.03674 ( 1254) hydrogen bonds : angle 4.57984 ( 3660) *********************** 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 305 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7935 (pmm) cc_final: 0.7583 (pmm) REVERT: A 1701 TRP cc_start: 0.7997 (p-90) cc_final: 0.7702 (p-90) REVERT: A 1756 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9052 (mp) REVERT: A 1967 MET cc_start: 0.8883 (mmm) cc_final: 0.8516 (mmm) REVERT: A 2012 MET cc_start: 0.8834 (mmm) cc_final: 0.8552 (tpp) REVERT: A 2324 LEU cc_start: 0.8284 (pp) cc_final: 0.8037 (tt) REVERT: A 2342 MET cc_start: 0.7420 (mtm) cc_final: 0.6966 (mtt) REVERT: A 2373 MET cc_start: 0.7864 (mtm) cc_final: 0.7599 (mtm) REVERT: A 2449 LEU cc_start: 0.8298 (tp) cc_final: 0.7994 (tp) REVERT: A 2615 MET cc_start: 0.8037 (ptt) cc_final: 0.7672 (mpp) REVERT: A 2799 MET cc_start: 0.8585 (ttm) cc_final: 0.8203 (ttm) REVERT: A 2994 MET cc_start: 0.7771 (tpt) cc_final: 0.7267 (tpt) REVERT: A 3187 PHE cc_start: 0.8495 (t80) cc_final: 0.8194 (t80) REVERT: A 3499 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7430 (pp30) REVERT: A 3500 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4957 (tpp) REVERT: A 3835 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9069 (mp) REVERT: A 3933 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8920 (mp0) REVERT: A 4043 MET cc_start: 0.8564 (mtm) cc_final: 0.8213 (mtm) REVERT: A 4339 MET cc_start: 0.9282 (tmm) cc_final: 0.8739 (tmm) REVERT: A 4380 LEU cc_start: 0.9118 (tp) cc_final: 0.8844 (tt) outliers start: 41 outliers final: 22 residues processed: 289 average time/residue: 0.1204 time to fit residues: 58.4460 Evaluate side-chains 264 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 1913 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1948 LEU 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 2568 VAL Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2810 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 3499 GLN Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3508 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 4028 THR Chi-restraints excluded: chain A residue 4545 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 250 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** A2005 GLN A2314 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN A4397 HIS A4526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.107837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082562 restraints weight = 70482.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.084900 restraints weight = 37779.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086491 restraints weight = 25895.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087507 restraints weight = 20366.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088209 restraints weight = 17598.388| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22340 Z= 0.122 Angle : 0.566 9.535 30308 Z= 0.278 Chirality : 0.040 0.203 3412 Planarity : 0.004 0.056 3883 Dihedral : 6.574 149.097 3014 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.70 % Allowed : 14.29 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.17), residues: 2699 helix: 1.90 (0.13), residues: 1523 sheet: -0.73 (0.33), residues: 244 loop : 0.33 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2118 TYR 0.021 0.001 TYR A2693 PHE 0.040 0.002 PHE A3496 TRP 0.012 0.001 TRP A2300 HIS 0.008 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00276 (22340) covalent geometry : angle 0.56569 (30308) hydrogen bonds : bond 0.03567 ( 1254) hydrogen bonds : angle 4.49412 ( 3660) *********************** 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 305 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7921 (pmm) cc_final: 0.7587 (pmm) REVERT: A 1701 TRP cc_start: 0.7903 (p-90) cc_final: 0.7547 (p-90) REVERT: A 1756 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9070 (mp) REVERT: A 1850 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7658 (tp-100) REVERT: A 1967 MET cc_start: 0.8776 (mmm) cc_final: 0.8426 (mmm) REVERT: A 2012 MET cc_start: 0.8898 (mmm) cc_final: 0.8639 (tpp) REVERT: A 2324 LEU cc_start: 0.8248 (pp) cc_final: 0.8008 (tt) REVERT: A 2342 MET cc_start: 0.7466 (mtm) cc_final: 0.6823 (mtt) REVERT: A 2373 MET cc_start: 0.7874 (mtm) cc_final: 0.7610 (mtm) REVERT: A 2449 LEU cc_start: 0.8269 (tp) cc_final: 0.8002 (tp) REVERT: A 2510 MET cc_start: 0.8856 (mtt) cc_final: 0.8624 (mtm) REVERT: A 2755 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8373 (tpp) REVERT: A 2799 MET cc_start: 0.8585 (ttm) cc_final: 0.8137 (ttm) REVERT: A 2897 LEU cc_start: 0.9026 (tp) cc_final: 0.8713 (tp) REVERT: A 2994 MET cc_start: 0.7777 (tpt) cc_final: 0.7304 (tpt) REVERT: A 3054 PHE cc_start: 0.8998 (t80) cc_final: 0.8743 (t80) REVERT: A 3502 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 3835 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9076 (mp) REVERT: A 3933 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8845 (mp0) REVERT: A 4043 MET cc_start: 0.8486 (mtm) cc_final: 0.8138 (mtm) REVERT: A 4296 MET cc_start: 0.8651 (tmm) cc_final: 0.8300 (tmm) REVERT: A 4339 MET cc_start: 0.9276 (tmm) cc_final: 0.8738 (tmm) REVERT: A 4380 LEU cc_start: 0.9117 (tp) cc_final: 0.8838 (tt) REVERT: A 4393 GLN cc_start: 0.8745 (pm20) cc_final: 0.8428 (mm-40) outliers start: 41 outliers final: 22 residues processed: 290 average time/residue: 0.1222 time to fit residues: 59.3828 Evaluate side-chains 262 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 1913 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2097 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 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 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3154 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4386 ASN A4526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.108688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083005 restraints weight = 69087.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085257 restraints weight = 38174.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086725 restraints weight = 26799.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087693 restraints weight = 21499.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088186 restraints weight = 18827.491| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22340 Z= 0.147 Angle : 0.587 10.901 30308 Z= 0.289 Chirality : 0.040 0.231 3412 Planarity : 0.004 0.054 3883 Dihedral : 6.573 146.805 3014 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.83 % Allowed : 15.45 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.17), residues: 2699 helix: 1.90 (0.13), residues: 1522 sheet: -0.59 (0.34), residues: 237 loop : 0.29 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2037 TYR 0.018 0.001 TYR A2693 PHE 0.048 0.002 PHE A2635 TRP 0.015 0.001 TRP A2300 HIS 0.006 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00332 (22340) covalent geometry : angle 0.58688 (30308) hydrogen bonds : bond 0.03599 ( 1254) hydrogen bonds : angle 4.48487 ( 3660) *********************** 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 280 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7944 (pmm) cc_final: 0.7609 (pmm) REVERT: A 1701 TRP cc_start: 0.7914 (p-90) cc_final: 0.7568 (p-90) REVERT: A 1756 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9094 (mp) REVERT: A 1967 MET cc_start: 0.8842 (mmm) cc_final: 0.8560 (mmm) REVERT: A 2324 LEU cc_start: 0.8308 (pp) cc_final: 0.8039 (tt) REVERT: A 2342 MET cc_start: 0.7588 (mtm) cc_final: 0.6953 (mtt) REVERT: A 2373 MET cc_start: 0.7990 (mtm) cc_final: 0.7701 (mtm) REVERT: A 2449 LEU cc_start: 0.8315 (tp) cc_final: 0.8059 (tp) REVERT: A 2737 ASP cc_start: 0.8762 (t0) cc_final: 0.8534 (m-30) REVERT: A 2755 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8426 (tpp) REVERT: A 2799 MET cc_start: 0.8708 (ttm) cc_final: 0.8505 (ttm) REVERT: A 2851 ASP cc_start: 0.8291 (t70) cc_final: 0.7969 (t0) REVERT: A 2897 LEU cc_start: 0.9047 (tp) cc_final: 0.8738 (tp) REVERT: A 2994 MET cc_start: 0.7819 (tpt) cc_final: 0.7357 (tpt) REVERT: A 3054 PHE cc_start: 0.9035 (t80) cc_final: 0.8786 (t80) REVERT: A 3187 PHE cc_start: 0.8514 (t80) cc_final: 0.8132 (t80) REVERT: A 3835 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9072 (mp) REVERT: A 3933 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8841 (mp0) REVERT: A 4043 MET cc_start: 0.8539 (mtm) cc_final: 0.8188 (mtm) REVERT: A 4339 MET cc_start: 0.9308 (tmm) cc_final: 0.8718 (tmm) REVERT: A 4380 LEU cc_start: 0.9133 (tp) cc_final: 0.8851 (tt) outliers start: 44 outliers final: 30 residues processed: 266 average time/residue: 0.1110 time to fit residues: 50.4496 Evaluate side-chains 264 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 1985 HIS Chi-restraints excluded: chain A residue 2005 GLN Chi-restraints excluded: chain A residue 2097 LEU 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 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 3005 LEU 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 4066 ILE Chi-restraints excluded: chain A residue 4182 LEU Chi-restraints excluded: chain A residue 4545 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 247 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 117 optimal weight: 0.1980 chunk 134 optimal weight: 0.0010 chunk 95 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN A3499 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.107658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082698 restraints weight = 70515.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085065 restraints weight = 37932.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086618 restraints weight = 25902.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087422 restraints weight = 20433.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088159 restraints weight = 17935.864| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22340 Z= 0.109 Angle : 0.572 9.776 30308 Z= 0.278 Chirality : 0.039 0.218 3412 Planarity : 0.004 0.050 3883 Dihedral : 6.419 146.891 3012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.54 % Allowed : 16.16 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.17), residues: 2699 helix: 1.98 (0.13), residues: 1523 sheet: -0.65 (0.34), residues: 242 loop : 0.33 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2921 TYR 0.016 0.001 TYR A4447 PHE 0.047 0.002 PHE A2635 TRP 0.016 0.001 TRP A2300 HIS 0.006 0.001 HIS A1921 Details of bonding type rmsd covalent geometry : bond 0.00245 (22340) covalent geometry : angle 0.57168 (30308) hydrogen bonds : bond 0.03416 ( 1254) hydrogen bonds : angle 4.37732 ( 3660) *********************** 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 291 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7904 (pmm) cc_final: 0.7525 (pmm) REVERT: A 1701 TRP cc_start: 0.7792 (p-90) cc_final: 0.7580 (p-90) REVERT: A 1756 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (mp) REVERT: A 1967 MET cc_start: 0.8800 (mmm) cc_final: 0.8554 (mmm) REVERT: A 2300 TRP cc_start: 0.8197 (m-10) cc_final: 0.7426 (m-10) REVERT: A 2324 LEU cc_start: 0.8242 (pp) cc_final: 0.7997 (tt) REVERT: A 2366 GLU cc_start: 0.8820 (tp30) cc_final: 0.8393 (tp30) REVERT: A 2373 MET cc_start: 0.7934 (mtm) cc_final: 0.7659 (mtm) REVERT: A 2737 ASP cc_start: 0.8732 (t0) cc_final: 0.8515 (m-30) REVERT: A 2755 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8487 (tpp) REVERT: A 2799 MET cc_start: 0.8631 (ttm) cc_final: 0.8383 (ttm) REVERT: A 2851 ASP cc_start: 0.8193 (t70) cc_final: 0.7877 (t0) REVERT: A 2885 ASP cc_start: 0.8203 (m-30) cc_final: 0.7484 (p0) REVERT: A 2897 LEU cc_start: 0.8978 (tp) cc_final: 0.8642 (tp) REVERT: A 2917 ASP cc_start: 0.8861 (t0) cc_final: 0.8377 (t0) REVERT: A 2994 MET cc_start: 0.7772 (tpt) cc_final: 0.7291 (tpt) REVERT: A 3054 PHE cc_start: 0.9010 (t80) cc_final: 0.8760 (t80) REVERT: A 3187 PHE cc_start: 0.8484 (t80) cc_final: 0.8269 (t80) REVERT: A 3835 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9059 (mp) REVERT: A 3873 ARG cc_start: 0.8733 (mmt180) cc_final: 0.8085 (mmt180) REVERT: A 3933 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8937 (mp0) REVERT: A 4043 MET cc_start: 0.8493 (mtm) cc_final: 0.8132 (mtm) REVERT: A 4339 MET cc_start: 0.9287 (tmm) cc_final: 0.8822 (tmm) REVERT: A 4380 LEU cc_start: 0.9099 (tp) cc_final: 0.8816 (tt) REVERT: A 4393 GLN cc_start: 0.8820 (pm20) cc_final: 0.8447 (mm-40) outliers start: 37 outliers final: 26 residues processed: 279 average time/residue: 0.1189 time to fit residues: 55.5878 Evaluate side-chains 258 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 1882 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1985 HIS Chi-restraints excluded: chain A residue 2097 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 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 2961 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3092 ASN Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3154 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 4094 VAL Chi-restraints excluded: chain A residue 4545 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 244 optimal weight: 0.0470 chunk 79 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- 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 ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082802 restraints weight = 70416.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085146 restraints weight = 38186.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086643 restraints weight = 26334.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087598 restraints weight = 20951.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088088 restraints weight = 18214.317| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2600 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= 0.116 Angle : 0.587 10.088 30308 Z= 0.285 Chirality : 0.040 0.215 3412 Planarity : 0.004 0.050 3883 Dihedral : 6.380 144.660 3012 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.54 % Allowed : 16.87 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.17), residues: 2699 helix: 2.01 (0.13), residues: 1523 sheet: -0.63 (0.35), residues: 230 loop : 0.34 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2037 TYR 0.030 0.001 TYR A3176 PHE 0.049 0.001 PHE A2635 TRP 0.019 0.001 TRP A2300 HIS 0.007 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00262 (22340) covalent geometry : angle 0.58728 (30308) hydrogen bonds : bond 0.03421 ( 1254) hydrogen bonds : angle 4.36795 ( 3660) *********************** 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 291 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7965 (pmm) cc_final: 0.7616 (pmm) REVERT: A 1701 TRP cc_start: 0.7768 (p-90) cc_final: 0.7525 (p-90) REVERT: A 1756 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 1967 MET cc_start: 0.8844 (mmm) cc_final: 0.8604 (mmm) REVERT: A 2012 MET cc_start: 0.8789 (mmm) cc_final: 0.8298 (tpp) REVERT: A 2300 TRP cc_start: 0.8287 (m-10) cc_final: 0.7513 (m-10) REVERT: A 2324 LEU cc_start: 0.8386 (pp) cc_final: 0.8129 (tt) REVERT: A 2366 GLU cc_start: 0.8828 (tp30) cc_final: 0.8386 (tp30) REVERT: A 2373 MET cc_start: 0.7945 (mtm) cc_final: 0.7652 (mtm) REVERT: A 2737 ASP cc_start: 0.8765 (t0) cc_final: 0.8538 (m-30) REVERT: A 2755 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8471 (tpp) REVERT: A 2799 MET cc_start: 0.8641 (ttm) cc_final: 0.8368 (ttm) REVERT: A 2851 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7897 (t0) REVERT: A 2885 ASP cc_start: 0.8126 (m-30) cc_final: 0.7392 (p0) REVERT: A 2897 LEU cc_start: 0.8966 (tp) cc_final: 0.8631 (tp) REVERT: A 2917 ASP cc_start: 0.8867 (t0) cc_final: 0.8360 (t0) REVERT: A 2994 MET cc_start: 0.7744 (tpt) cc_final: 0.7246 (tpt) REVERT: A 3054 PHE cc_start: 0.9016 (t80) cc_final: 0.8760 (t80) REVERT: A 3066 PHE cc_start: 0.8449 (m-80) cc_final: 0.8202 (m-10) REVERT: A 3835 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9080 (mp) REVERT: A 3873 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8408 (mmt180) REVERT: A 3933 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8966 (mp0) REVERT: A 4043 MET cc_start: 0.8495 (mtm) cc_final: 0.8113 (mtm) REVERT: A 4296 MET cc_start: 0.8775 (tpt) cc_final: 0.8451 (tpp) REVERT: A 4339 MET cc_start: 0.9304 (tmm) cc_final: 0.8789 (tmm) REVERT: A 4380 LEU cc_start: 0.9110 (tp) cc_final: 0.8822 (tt) REVERT: A 4393 GLN cc_start: 0.8871 (pm20) cc_final: 0.8454 (mm-40) outliers start: 37 outliers final: 29 residues processed: 276 average time/residue: 0.1316 time to fit residues: 59.6200 Evaluate side-chains 272 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 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 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 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 3115 LEU Chi-restraints excluded: chain A residue 3154 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 4094 VAL Chi-restraints excluded: chain A residue 4545 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 260 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3092 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080502 restraints weight = 71615.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082796 restraints weight = 38730.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084254 restraints weight = 26722.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085163 restraints weight = 21423.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085878 restraints weight = 18666.226| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22340 Z= 0.173 Angle : 0.637 15.978 30308 Z= 0.312 Chirality : 0.041 0.225 3412 Planarity : 0.004 0.057 3883 Dihedral : 6.401 140.492 3012 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.62 % Allowed : 16.87 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.17), residues: 2699 helix: 1.97 (0.13), residues: 1522 sheet: -0.63 (0.34), residues: 235 loop : 0.26 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2037 TYR 0.021 0.002 TYR A3183 PHE 0.049 0.002 PHE A2635 TRP 0.021 0.001 TRP A2300 HIS 0.007 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00393 (22340) covalent geometry : angle 0.63652 (30308) hydrogen bonds : bond 0.03634 ( 1254) hydrogen bonds : angle 4.46470 ( 3660) *********************** 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 285 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8030 (pmm) cc_final: 0.7659 (pmm) REVERT: A 1756 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (mp) REVERT: A 2145 MET cc_start: 0.8865 (mmm) cc_final: 0.8352 (mmm) REVERT: A 2300 TRP cc_start: 0.8369 (m-10) cc_final: 0.7633 (m-10) REVERT: A 2324 LEU cc_start: 0.8395 (pp) cc_final: 0.8127 (tt) REVERT: A 2366 GLU cc_start: 0.8881 (tp30) cc_final: 0.8443 (tp30) REVERT: A 2373 MET cc_start: 0.8101 (mtm) cc_final: 0.7866 (mtm) REVERT: A 2449 LEU cc_start: 0.8162 (tp) cc_final: 0.7879 (tp) REVERT: A 2684 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8305 (ptm160) REVERT: A 2737 ASP cc_start: 0.8820 (t0) cc_final: 0.8557 (m-30) REVERT: A 2755 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8439 (tpp) REVERT: A 2799 MET cc_start: 0.8793 (ttm) cc_final: 0.8499 (ttm) REVERT: A 2851 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 2885 ASP cc_start: 0.8269 (m-30) cc_final: 0.7445 (p0) REVERT: A 2917 ASP cc_start: 0.8953 (t0) cc_final: 0.8490 (t0) REVERT: A 2994 MET cc_start: 0.7780 (tpt) cc_final: 0.7247 (tpt) REVERT: A 3054 PHE cc_start: 0.9042 (t80) cc_final: 0.8789 (t80) REVERT: A 3066 PHE cc_start: 0.8409 (m-80) cc_final: 0.8152 (m-10) REVERT: A 3130 TYR cc_start: 0.8054 (t80) cc_final: 0.7759 (t80) REVERT: A 3835 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9106 (mp) REVERT: A 3933 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8856 (mp0) REVERT: A 4043 MET cc_start: 0.8565 (mtm) cc_final: 0.8192 (mtm) REVERT: A 4296 MET cc_start: 0.8830 (tpt) cc_final: 0.8465 (tpp) REVERT: A 4339 MET cc_start: 0.9333 (tmm) cc_final: 0.8785 (tmm) outliers start: 39 outliers final: 29 residues processed: 268 average time/residue: 0.1290 time to fit residues: 57.0610 Evaluate side-chains 265 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 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 2693 TYR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET 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 3115 LEU Chi-restraints excluded: chain A residue 3154 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 4094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 217 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** A3092 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.110129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084398 restraints weight = 68285.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086513 restraints weight = 38750.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087876 restraints weight = 27634.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088798 restraints weight = 22562.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089157 restraints weight = 19920.839| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2909 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 : 0.631 14.004 30308 Z= 0.307 Chirality : 0.041 0.218 3412 Planarity : 0.004 0.050 3883 Dihedral : 6.418 141.859 3012 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 17.37 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.17), residues: 2699 helix: 1.98 (0.13), residues: 1518 sheet: -0.79 (0.34), residues: 223 loop : 0.31 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3873 TYR 0.018 0.001 TYR A4447 PHE 0.050 0.002 PHE A2635 TRP 0.027 0.001 TRP A1701 HIS 0.006 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00335 (22340) covalent geometry : angle 0.63135 (30308) hydrogen bonds : bond 0.03587 ( 1254) hydrogen bonds : angle 4.44552 ( 3660) ********************** 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 271 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8088 (pmm) cc_final: 0.7682 (pmm) REVERT: A 1756 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9109 (mp) REVERT: A 2012 MET cc_start: 0.8767 (mmm) cc_final: 0.8561 (tpp) REVERT: A 2145 MET cc_start: 0.8904 (mmm) cc_final: 0.8362 (mmm) REVERT: A 2300 TRP cc_start: 0.8419 (m-10) cc_final: 0.7711 (m-10) REVERT: A 2366 GLU cc_start: 0.8877 (tp30) cc_final: 0.8344 (tp30) REVERT: A 2373 MET cc_start: 0.8065 (mtm) cc_final: 0.7832 (mtm) REVERT: A 2449 LEU cc_start: 0.8082 (tp) cc_final: 0.7677 (tp) REVERT: A 2737 ASP cc_start: 0.8819 (t0) cc_final: 0.8569 (m-30) REVERT: A 2755 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8485 (tpp) REVERT: A 2799 MET cc_start: 0.8760 (ttm) cc_final: 0.8201 (ttm) REVERT: A 2844 ARG cc_start: 0.9048 (ptp-110) cc_final: 0.8536 (ttp80) REVERT: A 2851 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8032 (t0) REVERT: A 2885 ASP cc_start: 0.8230 (m-30) cc_final: 0.7487 (p0) REVERT: A 2917 ASP cc_start: 0.8868 (t0) cc_final: 0.8410 (t0) REVERT: A 2994 MET cc_start: 0.7781 (tpt) cc_final: 0.7296 (tpt) REVERT: A 3054 PHE cc_start: 0.9019 (t80) cc_final: 0.8754 (t80) REVERT: A 3130 TYR cc_start: 0.8035 (t80) cc_final: 0.7832 (t80) REVERT: A 3835 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9036 (mp) REVERT: A 3933 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8914 (mp0) REVERT: A 4043 MET cc_start: 0.8493 (mtm) cc_final: 0.8124 (mtm) REVERT: A 4296 MET cc_start: 0.8711 (tpt) cc_final: 0.8309 (tpp) REVERT: A 4339 MET cc_start: 0.9344 (tmm) cc_final: 0.8846 (tmm) REVERT: A 4393 GLN cc_start: 0.8955 (pm20) cc_final: 0.8514 (mm-40) outliers start: 35 outliers final: 29 residues processed: 257 average time/residue: 0.1203 time to fit residues: 51.7568 Evaluate side-chains 267 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 2159 SER 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 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 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 3115 LEU Chi-restraints excluded: chain A residue 3154 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 4094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 190 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- 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** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3092 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3576 ASN A4549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.107187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080867 restraints weight = 68895.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.083146 restraints weight = 36232.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.084783 restraints weight = 25002.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085689 restraints weight = 19667.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086556 restraints weight = 17068.842| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3023 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= 0.116 Angle : 0.614 13.409 30308 Z= 0.296 Chirality : 0.040 0.202 3412 Planarity : 0.004 0.050 3883 Dihedral : 6.344 141.733 3012 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 17.41 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2699 helix: 2.05 (0.13), residues: 1516 sheet: -0.65 (0.35), residues: 223 loop : 0.32 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3873 TYR 0.017 0.001 TYR A4447 PHE 0.050 0.001 PHE A2635 TRP 0.021 0.001 TRP A2300 HIS 0.006 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00261 (22340) covalent geometry : angle 0.61380 (30308) hydrogen bonds : bond 0.03438 ( 1254) hydrogen bonds : angle 4.35560 ( 3660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.40 seconds wall clock time: 62 minutes 19.28 seconds (3739.28 seconds total)