Starting phenix.real_space_refine on Fri Sep 19 01:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm5_44688/09_2025/9bm5_44688.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 10 5.49 5 S 111 5.16 5 C 13839 2.51 5 N 3760 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 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: 21780 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2698, 21664 Classifications: {'peptide': 2698} Link IDs: {'PTRANS': 125, 'TRANS': 2572} Chain breaks: 6 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.31, per 1000 atoms: 0.20 Number of scatterers: 21780 At special positions: 0 Unit cell: (146.432, 158.08, 126.464, 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 10 15.00 O 4060 8.00 N 3760 7.00 C 13839 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: 1.75 Conformation dependent library (CDL) restraints added in 995.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5128 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 17 sheets defined 61.3% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.701A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.635A 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 1644 through 1646 No H-bonds generated for 'chain 'A' and resid 1644 through 1646' 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 1798 removed outlier: 3.881A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1841 removed outlier: 4.078A pdb=" N GLN A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.408A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 removed outlier: 3.510A pdb=" N LEU A2054 " --> pdb=" O ALA A2050 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.661A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.613A 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 2130 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: 4.216A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.540A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.770A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A2319 " --> pdb=" O LEU A2315 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.992A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.511A 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 2558 through 2562 removed outlier: 3.736A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.583A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.902A 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: 3.758A pdb=" N HIS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.806A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.583A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 5.156A 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: 3.649A 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 removed outlier: 3.529A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 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: 3.633A 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 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.504A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 3.549A pdb=" N PHE A3496 " --> pdb=" O THR A3492 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.832A 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: 3.614A 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 3730 removed outlier: 3.617A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) Processing helix chain 'A' and resid 3731 through 3733 No H-bonds generated for 'chain 'A' and resid 3731 through 3733' Processing helix chain 'A' and resid 3736 through 3755 Processing helix chain 'A' and resid 3763 through 3791 removed outlier: 3.996A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3819 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: 3.728A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3878 through 3895 removed outlier: 4.150A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) 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 3917 through 3921 Processing helix chain 'A' and resid 3928 through 3940 Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.792A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (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 4015 through 4018 removed outlier: 4.307A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4015 through 4018' Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.865A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.100A 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: 3.651A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.641A 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 Processing helix chain 'A' and resid 4175 through 4195 removed outlier: 3.979A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.667A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4325 through 4346 removed outlier: 4.242A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) 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 4505 Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.656A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) 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: 4.015A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 removed outlier: 3.684A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.855A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (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 2249 through 2251 removed outlier: 7.004A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 removed outlier: 3.708A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2325 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2617 through 2620 removed outlier: 6.280A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A2734 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.180A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 5.748A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A2933 " --> pdb=" O VAL A3064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 3.505A pdb=" N LEU A3634 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.628A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.796A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4568 through 4570 removed outlier: 3.837A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1254 hydrogen bonds defined for protein. 3666 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: 5.32 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: 1.03 - 1.18: 1 1.18 - 1.34: 7180 1.34 - 1.50: 5853 1.50 - 1.66: 9032 1.66 - 1.82: 185 Bond restraints: 22251 Sorted by residual: bond pdb=" CB PRO A2908 " pdb=" CG PRO A2908 " ideal model delta sigma weight residual 1.492 1.025 0.467 5.00e-02 4.00e+02 8.72e+01 bond pdb=" CG PRO A2908 " pdb=" CD PRO A2908 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.25e+01 bond pdb=" N PRO A2908 " pdb=" CA PRO A2908 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.20e-02 6.94e+03 2.83e+01 bond pdb=" N VAL A3215 " pdb=" CA VAL A3215 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.98e+00 bond pdb=" N ILE A3208 " pdb=" CA ILE A3208 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.93e+00 ... (remaining 22246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 30184 14.77 - 29.54: 0 29.54 - 44.31: 2 44.31 - 59.07: 0 59.07 - 73.84: 1 Bond angle restraints: 30187 Sorted by residual: angle pdb=" CB PRO A2908 " pdb=" CG PRO A2908 " pdb=" CD PRO A2908 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO A2908 " pdb=" CD PRO A2908 " pdb=" CG PRO A2908 " ideal model delta sigma weight residual 103.20 73.15 30.05 1.50e+00 4.44e-01 4.01e+02 angle pdb=" CA PRO A2908 " pdb=" CB PRO A2908 " pdb=" CG PRO A2908 " ideal model delta sigma weight residual 104.50 71.48 33.02 1.90e+00 2.77e-01 3.02e+02 angle pdb=" CA PRO A2908 " pdb=" N PRO A2908 " pdb=" CD PRO A2908 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 angle pdb=" N PRO A2908 " pdb=" CA PRO A2908 " pdb=" C PRO A2908 " ideal model delta sigma weight residual 111.03 120.16 -9.13 1.54e+00 4.22e-01 3.51e+01 ... (remaining 30182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 12918 32.97 - 65.93: 543 65.93 - 98.90: 41 98.90 - 131.86: 1 131.86 - 164.83: 1 Dihedral angle restraints: 13504 sinusoidal: 5612 harmonic: 7892 Sorted by residual: dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 135.17 164.83 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 59.17 -119.18 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" CA GLY A2229 " pdb=" C GLY A2229 " pdb=" N LYS A2230 " pdb=" CA LYS A2230 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 13501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3344 0.114 - 0.227: 53 0.227 - 0.341: 0 0.341 - 0.455: 0 0.455 - 0.568: 1 Chirality restraints: 3398 Sorted by residual: chirality pdb=" CG LEU A2452 " pdb=" CB LEU A2452 " pdb=" CD1 LEU A2452 " pdb=" CD2 LEU A2452 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" CB ILE A3881 " pdb=" CA ILE A3881 " pdb=" CG1 ILE A3881 " pdb=" CG2 ILE A3881 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A2108 " pdb=" CA ILE A2108 " pdb=" CG1 ILE A2108 " pdb=" CG2 ILE A2108 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 3395 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A2907 " 0.095 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO A2908 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO A2908 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A2908 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A3135 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A3136 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A3136 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A3136 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2327 " 0.070 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A2328 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A2328 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A2328 " 0.056 5.00e-02 4.00e+02 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 399 2.66 - 3.22: 21985 3.22 - 3.78: 36362 3.78 - 4.34: 47256 4.34 - 4.90: 75937 Nonbonded interactions: 181939 Sorted by model distance: nonbonded pdb=" O SER A1969 " pdb=" OE1 GLN A1973 " model vdw 2.096 3.040 nonbonded pdb=" CD2 LEU A4027 " pdb=" CD2 LEU A4058 " model vdw 2.104 3.880 nonbonded pdb=" O ALA A2497 " pdb=" OG SER A2501 " model vdw 2.138 3.040 nonbonded pdb=" O GLN A3792 " pdb=" OG1 THR A3796 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASP A2347 " pdb=" N LEU A2348 " model vdw 2.147 3.120 ... (remaining 181934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.570 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.467 22251 Z= 0.204 Angle : 0.873 73.842 30187 Z= 0.430 Chirality : 0.044 0.568 3398 Planarity : 0.006 0.131 3864 Dihedral : 17.208 164.829 8376 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.21 % Allowed : 23.03 % Favored : 76.76 % 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: 1.01 (0.16), residues: 2684 helix: 1.49 (0.13), residues: 1501 sheet: -1.23 (0.35), residues: 215 loop : -0.03 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2811 TYR 0.053 0.002 TYR A2517 PHE 0.036 0.002 PHE A1926 TRP 0.043 0.002 TRP A3489 HIS 0.007 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00531 (22251) covalent geometry : angle 0.87277 (30187) hydrogen bonds : bond 0.13938 ( 1254) hydrogen bonds : angle 5.99680 ( 3666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4464 TRP cc_start: 0.7079 (m-10) cc_final: 0.6691 (m100) outliers start: 5 outliers final: 2 residues processed: 306 average time/residue: 0.1278 time to fit residues: 64.5025 Evaluate side-chains 300 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 4447 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1841 GLN A1894 GLN A2463 HIS A2849 ASN A2930 GLN ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3202 ASN A3988 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4108 GLN A4381 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.129450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104750 restraints weight = 49941.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107967 restraints weight = 24828.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110154 restraints weight = 15808.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.111491 restraints weight = 11757.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112449 restraints weight = 9729.675| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22251 Z= 0.177 Angle : 0.627 8.626 30187 Z= 0.318 Chirality : 0.042 0.185 3398 Planarity : 0.005 0.073 3864 Dihedral : 7.715 162.358 3024 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.59 % Allowed : 19.65 % Favored : 76.76 % 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: 1.09 (0.16), residues: 2684 helix: 1.49 (0.13), residues: 1518 sheet: -1.19 (0.34), residues: 223 loop : 0.09 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4176 TYR 0.027 0.002 TYR A2901 PHE 0.028 0.002 PHE A1926 TRP 0.021 0.002 TRP A4376 HIS 0.005 0.001 HIS A2218 Details of bonding type rmsd covalent geometry : bond 0.00402 (22251) covalent geometry : angle 0.62695 (30187) hydrogen bonds : bond 0.04715 ( 1254) hydrogen bonds : angle 5.00513 ( 3666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1629 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4778 (p90) REVERT: A 1923 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 1945 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 2496 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6281 (t80) REVERT: A 2816 LEU cc_start: 0.8054 (mt) cc_final: 0.7846 (mt) REVERT: A 3011 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3503 (tt) REVERT: A 3094 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: A 3113 MET cc_start: 0.6950 (mmm) cc_final: 0.6385 (mpp) REVERT: A 3489 TRP cc_start: 0.5372 (m100) cc_final: 0.4715 (m-10) REVERT: A 4339 MET cc_start: 0.7202 (tpp) cc_final: 0.6983 (tpt) outliers start: 86 outliers final: 56 residues processed: 392 average time/residue: 0.1265 time to fit residues: 81.6452 Evaluate side-chains 366 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 304 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3011 LEU Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3566 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3881 ILE Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 0.0000 chunk 256 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN A1894 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.132089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107032 restraints weight = 50559.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110376 restraints weight = 25310.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.112632 restraints weight = 16218.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113985 restraints weight = 12105.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.115005 restraints weight = 10035.965| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22251 Z= 0.123 Angle : 0.565 9.126 30187 Z= 0.284 Chirality : 0.040 0.176 3398 Planarity : 0.004 0.065 3864 Dihedral : 7.223 153.064 3022 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.25 % Allowed : 20.32 % Favored : 76.43 % 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: 1.33 (0.16), residues: 2684 helix: 1.75 (0.13), residues: 1513 sheet: -1.18 (0.33), residues: 229 loop : 0.13 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4176 TYR 0.026 0.001 TYR A2901 PHE 0.022 0.001 PHE A1926 TRP 0.018 0.001 TRP A1701 HIS 0.004 0.001 HIS A2445 Details of bonding type rmsd covalent geometry : bond 0.00272 (22251) covalent geometry : angle 0.56542 (30187) hydrogen bonds : bond 0.04173 ( 1254) hydrogen bonds : angle 4.72241 ( 3666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 349 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1856 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6406 (mm-40) REVERT: A 1923 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8650 (mm) REVERT: A 1967 MET cc_start: 0.8199 (tpt) cc_final: 0.7973 (tpt) REVERT: A 2034 LYS cc_start: 0.9334 (mttt) cc_final: 0.8883 (tmtt) REVERT: A 2496 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6095 (t80) REVERT: A 2510 MET cc_start: 0.8606 (mtt) cc_final: 0.8282 (mtp) REVERT: A 3011 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.3301 (tt) REVERT: A 3051 TYR cc_start: 0.7203 (t80) cc_final: 0.7003 (t80) REVERT: A 3094 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: A 3113 MET cc_start: 0.6942 (mmm) cc_final: 0.6265 (mpp) REVERT: A 3489 TRP cc_start: 0.5523 (m100) cc_final: 0.4938 (m-10) REVERT: A 3613 SER cc_start: 0.7282 (t) cc_final: 0.6829 (p) REVERT: A 3913 GLU cc_start: 0.8346 (tt0) cc_final: 0.7864 (mp0) REVERT: A 4012 ASN cc_start: 0.7745 (t0) cc_final: 0.7503 (t0) REVERT: A 4339 MET cc_start: 0.7109 (tpp) cc_final: 0.6901 (tpp) REVERT: A 4377 MET cc_start: 0.8125 (mmm) cc_final: 0.7484 (tpp) REVERT: A 4378 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6777 (mmt180) REVERT: A 4542 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7734 (pt0) outliers start: 78 outliers final: 45 residues processed: 400 average time/residue: 0.1307 time to fit residues: 84.6565 Evaluate side-chains 364 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1856 GLN Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3011 LEU Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3881 ILE Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4554 ASP Chi-restraints excluded: chain A residue 4614 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 137 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 255 optimal weight: 10.0000 chunk 211 optimal weight: 0.0370 chunk 110 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1651 GLN A1850 GLN A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3198 GLN A3535 HIS A3538 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.129562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104763 restraints weight = 50129.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107978 restraints weight = 25001.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110142 restraints weight = 16001.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111509 restraints weight = 11941.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112461 restraints weight = 9891.326| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22251 Z= 0.176 Angle : 0.607 9.698 30187 Z= 0.303 Chirality : 0.042 0.230 3398 Planarity : 0.004 0.056 3864 Dihedral : 7.237 154.742 3022 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.42 % Allowed : 20.82 % Favored : 74.76 % 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: 1.21 (0.16), residues: 2684 helix: 1.66 (0.13), residues: 1512 sheet: -1.24 (0.33), residues: 234 loop : 0.07 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3695 TYR 0.024 0.002 TYR A3103 PHE 0.023 0.002 PHE A1926 TRP 0.018 0.002 TRP A1701 HIS 0.004 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00410 (22251) covalent geometry : angle 0.60709 (30187) hydrogen bonds : bond 0.04242 ( 1254) hydrogen bonds : angle 4.75610 ( 3666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 328 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1629 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4937 (p90) REVERT: A 1923 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 1945 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 1967 MET cc_start: 0.8249 (tpt) cc_final: 0.8002 (tpt) REVERT: A 2034 LYS cc_start: 0.9403 (mttt) cc_final: 0.8931 (tmtt) REVERT: A 2350 TYR cc_start: 0.8838 (m-80) cc_final: 0.8606 (m-10) REVERT: A 2496 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 2510 MET cc_start: 0.8629 (mtt) cc_final: 0.8313 (mtp) REVERT: A 3094 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: A 3113 MET cc_start: 0.6991 (mmm) cc_final: 0.6349 (mpp) REVERT: A 3489 TRP cc_start: 0.5575 (m100) cc_final: 0.5128 (m-10) REVERT: A 3913 GLU cc_start: 0.8415 (tt0) cc_final: 0.7868 (mp0) REVERT: A 4012 ASN cc_start: 0.7852 (t0) cc_final: 0.7587 (t0) REVERT: A 4377 MET cc_start: 0.8133 (mmm) cc_final: 0.7420 (tpp) REVERT: A 4378 ARG cc_start: 0.7030 (mmt180) cc_final: 0.6620 (mmt180) outliers start: 106 outliers final: 70 residues processed: 398 average time/residue: 0.1316 time to fit residues: 85.3175 Evaluate side-chains 387 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 312 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3566 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3694 SER Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3881 ILE Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4554 ASP Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 114 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 202 optimal weight: 0.0370 chunk 197 optimal weight: 6.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS ** A3714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.131778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106838 restraints weight = 50600.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.110170 restraints weight = 25282.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112358 restraints weight = 16144.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113766 restraints weight = 12044.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114731 restraints weight = 9949.483| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22251 Z= 0.122 Angle : 0.573 10.373 30187 Z= 0.284 Chirality : 0.040 0.179 3398 Planarity : 0.004 0.055 3864 Dihedral : 7.020 148.202 3022 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.55 % Allowed : 22.32 % Favored : 74.13 % 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: 1.30 (0.16), residues: 2684 helix: 1.77 (0.13), residues: 1513 sheet: -1.30 (0.33), residues: 223 loop : 0.05 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4428 TYR 0.033 0.002 TYR A2517 PHE 0.021 0.001 PHE A1926 TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A2445 Details of bonding type rmsd covalent geometry : bond 0.00275 (22251) covalent geometry : angle 0.57293 (30187) hydrogen bonds : bond 0.03946 ( 1254) hydrogen bonds : angle 4.62702 ( 3666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1923 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8630 (mm) REVERT: A 1945 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7184 (t80) REVERT: A 1967 MET cc_start: 0.8166 (tpt) cc_final: 0.7783 (tpt) REVERT: A 1973 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 2034 LYS cc_start: 0.9385 (mttt) cc_final: 0.8918 (tmtt) REVERT: A 2152 GLU cc_start: 0.8176 (tp30) cc_final: 0.7944 (tp30) REVERT: A 2496 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 2510 MET cc_start: 0.8638 (mtt) cc_final: 0.8318 (mtp) REVERT: A 3094 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: A 3104 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: A 3113 MET cc_start: 0.7022 (mmm) cc_final: 0.6421 (mpp) REVERT: A 3209 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7306 (mptt) REVERT: A 3489 TRP cc_start: 0.5503 (m100) cc_final: 0.5003 (m-10) REVERT: A 4012 ASN cc_start: 0.7743 (t0) cc_final: 0.7487 (t0) REVERT: A 4129 GLU cc_start: 0.7828 (tp30) cc_final: 0.7604 (tp30) REVERT: A 4157 MET cc_start: 0.9018 (mtt) cc_final: 0.8755 (mtm) REVERT: A 4321 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7750 (pp) REVERT: A 4377 MET cc_start: 0.8107 (mmm) cc_final: 0.7525 (tpp) REVERT: A 4378 ARG cc_start: 0.6963 (mmt180) cc_final: 0.6593 (mmt180) REVERT: A 4542 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7710 (pt0) outliers start: 85 outliers final: 55 residues processed: 387 average time/residue: 0.1387 time to fit residues: 87.3444 Evaluate side-chains 376 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4554 ASP Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 176 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 231 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 197 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.132672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107762 restraints weight = 50527.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111094 restraints weight = 25186.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.113352 restraints weight = 16097.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114749 restraints weight = 11947.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.115716 restraints weight = 9867.795| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22251 Z= 0.119 Angle : 0.567 10.664 30187 Z= 0.280 Chirality : 0.040 0.187 3398 Planarity : 0.004 0.058 3864 Dihedral : 6.852 144.045 3022 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.84 % Allowed : 22.40 % Favored : 73.76 % 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: 1.34 (0.16), residues: 2684 helix: 1.80 (0.13), residues: 1518 sheet: -1.36 (0.33), residues: 227 loop : 0.08 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4428 TYR 0.034 0.001 TYR A2517 PHE 0.020 0.001 PHE A1926 TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A2445 Details of bonding type rmsd covalent geometry : bond 0.00268 (22251) covalent geometry : angle 0.56671 (30187) hydrogen bonds : bond 0.03790 ( 1254) hydrogen bonds : angle 4.53893 ( 3666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 343 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1629 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4744 (p90) REVERT: A 1923 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8633 (mm) REVERT: A 1945 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7253 (t80) REVERT: A 1967 MET cc_start: 0.8154 (tpt) cc_final: 0.7771 (tpt) REVERT: A 1973 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: A 2034 LYS cc_start: 0.9386 (mttt) cc_final: 0.8929 (tmtt) REVERT: A 2152 GLU cc_start: 0.8188 (tp30) cc_final: 0.7983 (tp30) REVERT: A 2350 TYR cc_start: 0.8796 (m-80) cc_final: 0.8490 (m-10) REVERT: A 2496 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6175 (t80) REVERT: A 2510 MET cc_start: 0.8613 (mtt) cc_final: 0.8322 (mtp) REVERT: A 2869 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.8038 (tpp-160) REVERT: A 2876 TRP cc_start: 0.4896 (m100) cc_final: 0.4623 (m100) REVERT: A 3094 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7182 (m-10) REVERT: A 3104 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6495 (mp10) REVERT: A 3113 MET cc_start: 0.7063 (mmm) cc_final: 0.6489 (mpp) REVERT: A 3209 LYS cc_start: 0.7575 (mmmt) cc_final: 0.7330 (mptt) REVERT: A 3489 TRP cc_start: 0.5544 (m100) cc_final: 0.5278 (m-10) REVERT: A 3791 MET cc_start: 0.8358 (mtm) cc_final: 0.7658 (mmm) REVERT: A 4012 ASN cc_start: 0.7682 (t0) cc_final: 0.7329 (t0) REVERT: A 4321 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7634 (pp) REVERT: A 4377 MET cc_start: 0.8074 (mmm) cc_final: 0.7618 (tpp) REVERT: A 4422 LYS cc_start: 0.7529 (mmtm) cc_final: 0.7230 (mmtm) REVERT: A 4477 GLN cc_start: 0.8941 (mp10) cc_final: 0.8461 (pm20) REVERT: A 4542 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7725 (pt0) outliers start: 92 outliers final: 66 residues processed: 401 average time/residue: 0.1351 time to fit residues: 87.5675 Evaluate side-chains 396 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 321 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2933 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3950 LYS Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 40 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.132170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107010 restraints weight = 50838.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.110299 restraints weight = 25614.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.112556 restraints weight = 16510.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113903 restraints weight = 12326.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114906 restraints weight = 10233.263| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22251 Z= 0.121 Angle : 0.576 8.497 30187 Z= 0.283 Chirality : 0.040 0.241 3398 Planarity : 0.004 0.046 3864 Dihedral : 6.802 142.777 3022 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.55 % Allowed : 22.99 % Favored : 73.47 % 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: 1.33 (0.16), residues: 2684 helix: 1.80 (0.13), residues: 1521 sheet: -1.34 (0.33), residues: 227 loop : 0.06 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3007 TYR 0.038 0.002 TYR A2517 PHE 0.019 0.001 PHE A1926 TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00275 (22251) covalent geometry : angle 0.57604 (30187) hydrogen bonds : bond 0.03773 ( 1254) hydrogen bonds : angle 4.49398 ( 3666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 333 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1629 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4766 (p90) REVERT: A 1923 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 1941 MET cc_start: 0.7757 (tmm) cc_final: 0.7175 (tmm) REVERT: A 1945 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 1973 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: A 2034 LYS cc_start: 0.9395 (mttt) cc_final: 0.8959 (tmtt) REVERT: A 2350 TYR cc_start: 0.8814 (m-80) cc_final: 0.8442 (m-10) REVERT: A 2496 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6159 (t80) REVERT: A 2510 MET cc_start: 0.8614 (mtt) cc_final: 0.8315 (mtp) REVERT: A 2876 TRP cc_start: 0.4867 (m100) cc_final: 0.4650 (m100) REVERT: A 3094 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: A 3104 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: A 3113 MET cc_start: 0.7093 (mmm) cc_final: 0.6530 (mpp) REVERT: A 3209 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7319 (mptt) REVERT: A 3489 TRP cc_start: 0.5706 (m100) cc_final: 0.5409 (m-10) REVERT: A 3611 ARG cc_start: 0.8723 (mtp180) cc_final: 0.8015 (mtp85) REVERT: A 3791 MET cc_start: 0.8371 (mtm) cc_final: 0.7668 (mmm) REVERT: A 4012 ASN cc_start: 0.7681 (t0) cc_final: 0.7420 (t0) REVERT: A 4043 MET cc_start: 0.7783 (mtp) cc_final: 0.7542 (mtp) REVERT: A 4321 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7773 (pp) REVERT: A 4477 GLN cc_start: 0.8936 (mt0) cc_final: 0.8428 (pm20) REVERT: A 4542 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7689 (pt0) outliers start: 85 outliers final: 62 residues processed: 388 average time/residue: 0.1326 time to fit residues: 83.2443 Evaluate side-chains 383 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 312 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3950 LYS Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS A3535 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.130802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105628 restraints weight = 51311.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.108815 restraints weight = 26097.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111043 restraints weight = 17001.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112372 restraints weight = 12760.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.113312 restraints weight = 10620.615| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22251 Z= 0.153 Angle : 0.602 9.212 30187 Z= 0.300 Chirality : 0.041 0.230 3398 Planarity : 0.004 0.063 3864 Dihedral : 6.917 144.198 3022 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.67 % Allowed : 22.95 % Favored : 73.38 % 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: 1.24 (0.16), residues: 2684 helix: 1.73 (0.13), residues: 1515 sheet: -1.31 (0.32), residues: 235 loop : 0.01 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3007 TYR 0.043 0.002 TYR A2517 PHE 0.056 0.002 PHE A2727 TRP 0.017 0.002 TRP A1701 HIS 0.004 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00357 (22251) covalent geometry : angle 0.60230 (30187) hydrogen bonds : bond 0.03979 ( 1254) hydrogen bonds : angle 4.53324 ( 3666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 332 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1629 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4827 (p90) REVERT: A 1923 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 1941 MET cc_start: 0.7799 (tmm) cc_final: 0.7150 (tmm) REVERT: A 1945 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 1973 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: A 2034 LYS cc_start: 0.9393 (mttt) cc_final: 0.8959 (tmtt) REVERT: A 2179 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7046 (mtm110) REVERT: A 2350 TYR cc_start: 0.8828 (m-80) cc_final: 0.8448 (m-10) REVERT: A 2496 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6350 (t80) REVERT: A 2510 MET cc_start: 0.8603 (mtt) cc_final: 0.8282 (mtp) REVERT: A 3004 PHE cc_start: 0.5641 (m-10) cc_final: 0.4750 (m-10) REVERT: A 3094 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: A 3104 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: A 3113 MET cc_start: 0.7099 (mmm) cc_final: 0.6618 (mpp) REVERT: A 3209 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7336 (mptt) REVERT: A 3489 TRP cc_start: 0.5718 (m100) cc_final: 0.5452 (m-10) REVERT: A 4012 ASN cc_start: 0.7733 (t0) cc_final: 0.7419 (t0) REVERT: A 4043 MET cc_start: 0.7846 (mtp) cc_final: 0.7617 (mtp) REVERT: A 4128 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7897 (ttm) REVERT: A 4321 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7897 (pp) REVERT: A 4377 MET cc_start: 0.8166 (mmm) cc_final: 0.7618 (tpp) REVERT: A 4477 GLN cc_start: 0.8986 (mt0) cc_final: 0.8447 (pm20) REVERT: A 4542 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7707 (pt0) outliers start: 88 outliers final: 67 residues processed: 386 average time/residue: 0.1351 time to fit residues: 85.4018 Evaluate side-chains 395 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 318 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3566 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 48 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS A3535 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.107549 restraints weight = 50987.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110870 restraints weight = 25581.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.113089 restraints weight = 16389.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114441 restraints weight = 12227.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115430 restraints weight = 10130.893| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22251 Z= 0.125 Angle : 0.605 13.288 30187 Z= 0.296 Chirality : 0.041 0.215 3398 Planarity : 0.004 0.052 3864 Dihedral : 6.783 138.997 3022 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.30 % Allowed : 23.70 % Favored : 73.01 % 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: 1.30 (0.16), residues: 2684 helix: 1.77 (0.13), residues: 1513 sheet: -1.24 (0.33), residues: 225 loop : 0.03 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4428 TYR 0.048 0.002 TYR A2517 PHE 0.049 0.001 PHE A2727 TRP 0.019 0.001 TRP A1701 HIS 0.006 0.001 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00287 (22251) covalent geometry : angle 0.60497 (30187) hydrogen bonds : bond 0.03787 ( 1254) hydrogen bonds : angle 4.47545 ( 3666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 329 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1941 MET cc_start: 0.7801 (tmm) cc_final: 0.7104 (tmm) REVERT: A 1945 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 1973 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: A 2034 LYS cc_start: 0.9405 (mttt) cc_final: 0.8930 (tmtt) REVERT: A 2350 TYR cc_start: 0.8810 (m-80) cc_final: 0.8424 (m-10) REVERT: A 2496 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6236 (t80) REVERT: A 2510 MET cc_start: 0.8593 (mtt) cc_final: 0.8316 (mtp) REVERT: A 2876 TRP cc_start: 0.4688 (m100) cc_final: 0.4448 (m100) REVERT: A 2973 ASP cc_start: 0.6898 (m-30) cc_final: 0.6608 (m-30) REVERT: A 3004 PHE cc_start: 0.5634 (m-10) cc_final: 0.4752 (m-10) REVERT: A 3051 TYR cc_start: 0.7274 (t80) cc_final: 0.7023 (t80) REVERT: A 3094 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: A 3104 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6527 (mp10) REVERT: A 3113 MET cc_start: 0.6998 (mmm) cc_final: 0.6275 (mpp) REVERT: A 3209 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7330 (mptt) REVERT: A 3489 TRP cc_start: 0.5754 (m100) cc_final: 0.5474 (m-10) REVERT: A 4012 ASN cc_start: 0.7734 (t0) cc_final: 0.7407 (t0) REVERT: A 4043 MET cc_start: 0.7767 (mtp) cc_final: 0.7504 (mtp) REVERT: A 4128 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7976 (ttm) REVERT: A 4321 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7854 (pp) REVERT: A 4377 MET cc_start: 0.8187 (mmm) cc_final: 0.7611 (tpp) REVERT: A 4477 GLN cc_start: 0.8935 (mt0) cc_final: 0.8390 (pm20) REVERT: A 4542 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7716 (pt0) outliers start: 79 outliers final: 61 residues processed: 376 average time/residue: 0.1325 time to fit residues: 81.1345 Evaluate side-chains 384 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1866 PHE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3566 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 251 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A4100 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.132655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107766 restraints weight = 50890.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111080 restraints weight = 25599.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.113292 restraints weight = 16373.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.114696 restraints weight = 12192.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.115557 restraints weight = 10074.223| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22251 Z= 0.126 Angle : 0.603 11.081 30187 Z= 0.295 Chirality : 0.041 0.230 3398 Planarity : 0.004 0.065 3864 Dihedral : 6.732 137.552 3022 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.05 % Allowed : 24.16 % Favored : 72.80 % 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: 1.33 (0.16), residues: 2684 helix: 1.78 (0.13), residues: 1519 sheet: -1.20 (0.33), residues: 225 loop : 0.05 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3160 TYR 0.050 0.002 TYR A2517 PHE 0.050 0.001 PHE A2727 TRP 0.020 0.001 TRP A1701 HIS 0.011 0.001 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00289 (22251) covalent geometry : angle 0.60256 (30187) hydrogen bonds : bond 0.03722 ( 1254) hydrogen bonds : angle 4.43946 ( 3666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 332 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1941 MET cc_start: 0.7805 (tmm) cc_final: 0.7059 (tmm) REVERT: A 1945 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7275 (t80) REVERT: A 1973 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: A 2034 LYS cc_start: 0.9411 (mttt) cc_final: 0.8966 (tmtt) REVERT: A 2350 TYR cc_start: 0.8799 (m-80) cc_final: 0.8358 (m-10) REVERT: A 2496 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 2510 MET cc_start: 0.8577 (mtt) cc_final: 0.8305 (mtp) REVERT: A 3004 PHE cc_start: 0.5603 (m-10) cc_final: 0.4656 (m-10) REVERT: A 3094 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: A 3104 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: A 3113 MET cc_start: 0.7001 (mmm) cc_final: 0.6279 (mpp) REVERT: A 3209 LYS cc_start: 0.7619 (mmmt) cc_final: 0.7356 (mptt) REVERT: A 3489 TRP cc_start: 0.5743 (m100) cc_final: 0.5497 (m-10) REVERT: A 4012 ASN cc_start: 0.7714 (t0) cc_final: 0.7362 (t0) REVERT: A 4377 MET cc_start: 0.8091 (mmm) cc_final: 0.7577 (tpp) REVERT: A 4477 GLN cc_start: 0.8947 (mt0) cc_final: 0.8412 (pm20) REVERT: A 4542 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7716 (pt0) outliers start: 73 outliers final: 60 residues processed: 377 average time/residue: 0.1317 time to fit residues: 80.8987 Evaluate side-chains 388 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1950 GLN Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2989 LYS Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3063 HIS Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3119 ASN Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3566 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4320 TRP Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4436 GLN Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4450 THR Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 31 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2637 HIS ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A3636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108323 restraints weight = 50827.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111598 restraints weight = 25559.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113850 restraints weight = 16434.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.115278 restraints weight = 12250.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.116014 restraints weight = 10087.033| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22251 Z= 0.124 Angle : 0.610 14.130 30187 Z= 0.297 Chirality : 0.041 0.228 3398 Planarity : 0.004 0.047 3864 Dihedral : 6.693 135.953 3022 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 24.28 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.16), residues: 2684 helix: 1.79 (0.13), residues: 1519 sheet: -1.19 (0.33), residues: 225 loop : 0.05 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3160 TYR 0.052 0.002 TYR A2517 PHE 0.046 0.001 PHE A2727 TRP 0.041 0.002 TRP A2876 HIS 0.013 0.001 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00283 (22251) covalent geometry : angle 0.61037 (30187) hydrogen bonds : bond 0.03702 ( 1254) hydrogen bonds : angle 4.42917 ( 3666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.56 seconds wall clock time: 70 minutes 52.70 seconds (4252.70 seconds total)