Starting phenix.real_space_refine on Thu Jun 19 08:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm3_44686/06_2025/9bm3_44686.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 111 5.16 5 C 13892 2.51 5 N 3777 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.40, per 1000 atoms: 0.57 Number of scatterers: 21867 At special positions: 0 Unit cell: (146.432, 158.08, 122.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4078 8.00 N 3777 7.00 C 13892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.5 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 18 sheets defined 61.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.775A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1649 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1796 Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1841 removed outlier: 4.163A pdb=" N GLN A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 removed outlier: 3.552A pdb=" N VAL A1916 " --> pdb=" O LYS A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.610A 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: 4.446A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2190 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: 3.629A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.772A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.542A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.508A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.724A 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 removed outlier: 3.556A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.697A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2548 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.512A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.554A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2601 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.129A 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 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 5.259A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.516A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A2779 " --> pdb=" O GLU A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.759A 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: 3.692A pdb=" N LEU A2916 " --> pdb=" O PHE A2912 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2984 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.972A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3062 removed outlier: 3.520A pdb=" N LEU A3050 " --> pdb=" O SER A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 removed outlier: 3.572A pdb=" N ARG A3088 " --> pdb=" O ALA A3084 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.686A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A3196 " --> pdb=" O SER A3192 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 5.141A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.732A 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: 3.760A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3629 Processing helix chain 'A' and resid 3644 through 3651 removed outlier: 4.440A pdb=" N VAL A3648 " --> pdb=" O VAL A3644 " (cutoff:3.500A) Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3737 removed outlier: 3.693A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3737 through 3755 Processing helix chain 'A' and resid 3766 through 3791 Processing helix chain 'A' and resid 3793 through 3818 removed outlier: 3.911A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.539A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 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 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.814A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 3.991A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 removed outlier: 3.602A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.945A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.769A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.243A 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: 3.690A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.659A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.514A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.503A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.544A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4407 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 3.939A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.502A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 7.876A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.589A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.776A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1928 through 1931 removed outlier: 6.441A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (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 2253 removed outlier: 6.842A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.260A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 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: 5.934A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.639A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.971A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.205A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.229A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.541A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4509 through 4510 Processing sheet with id=AB9, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.869A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3672 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: 12.39 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5686 1.33 - 1.46: 4345 1.46 - 1.58: 12107 1.58 - 1.70: 17 1.70 - 1.82: 185 Bond restraints: 22340 Sorted by residual: bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" N ILE A2049 " pdb=" CA ILE A2049 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.83e+00 bond pdb=" N GLY A2089 " pdb=" CA GLY A2089 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.06e-02 8.90e+03 7.75e+00 bond pdb=" N LYS A1878 " pdb=" CA LYS A1878 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.53e+00 ... (remaining 22335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 29996 2.76 - 5.51: 270 5.51 - 8.27: 23 8.27 - 11.02: 15 11.02 - 13.78: 4 Bond angle restraints: 30308 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 128.63 11.24 1.00e+00 1.00e+00 1.26e+02 angle pdb=" CA PRO A2812 " pdb=" N PRO A2812 " pdb=" CD PRO A2812 " ideal model delta sigma weight residual 112.00 99.53 12.47 1.40e+00 5.10e-01 7.93e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 128.00 8.83 1.00e+00 1.00e+00 7.80e+01 angle pdb=" CA PRO A1848 " pdb=" N PRO A1848 " pdb=" CD PRO A1848 " ideal model delta sigma weight residual 112.00 103.36 8.64 1.40e+00 5.10e-01 3.81e+01 angle pdb=" CA PRO A2020 " pdb=" N PRO A2020 " pdb=" CD PRO A2020 " ideal model delta sigma weight residual 112.00 104.95 7.05 1.40e+00 5.10e-01 2.54e+01 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.51: 12817 29.51 - 59.03: 647 59.03 - 88.54: 74 88.54 - 118.05: 2 118.05 - 147.56: 2 Dihedral angle restraints: 13542 sinusoidal: 5612 harmonic: 7930 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 87.56 -147.56 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 164.24 135.76 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" CA VAL A3660 " pdb=" C VAL A3660 " pdb=" N LEU A3661 " pdb=" CA LEU A3661 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 13539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2815 0.051 - 0.101: 504 0.101 - 0.152: 88 0.152 - 0.202: 2 0.202 - 0.253: 3 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CG LEU A4113 " pdb=" CB LEU A4113 " pdb=" CD1 LEU A4113 " pdb=" CD2 LEU A4113 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A1880 " pdb=" CA VAL A1880 " pdb=" CG1 VAL A1880 " pdb=" CG2 VAL A1880 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU A1879 " pdb=" N LEU A1879 " pdb=" C LEU A1879 " pdb=" CB LEU A1879 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3409 not shown) Planarity restraints: 3883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A2811 " 0.093 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A2812 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A2812 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A2812 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1847 " -0.081 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO A1848 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO A1848 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1848 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A3137 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " 0.047 5.00e-02 4.00e+02 ... (remaining 3880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 610 2.71 - 3.26: 23423 3.26 - 3.81: 37138 3.81 - 4.35: 45481 4.35 - 4.90: 75210 Nonbonded interactions: 181862 Sorted by model distance: nonbonded pdb=" OH TYR A2967 " pdb=" OD2 ASP A2975 " model vdw 2.163 3.040 nonbonded pdb=" NH1 ARG A4176 " pdb=" OD1 ASP A4220 " model vdw 2.177 3.120 nonbonded pdb=" OE2 GLU A1763 " pdb=" OH TYR A1845 " model vdw 2.217 3.040 nonbonded pdb=" O SER A2623 " pdb=" OG1 THR A2626 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A4288 " pdb=" OG SER A4319 " model vdw 2.227 3.040 ... (remaining 181857 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 52.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 22340 Z= 0.188 Angle : 0.682 13.777 30308 Z= 0.370 Chirality : 0.041 0.253 3412 Planarity : 0.005 0.132 3883 Dihedral : 16.652 147.564 8390 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.54 % Allowed : 16.49 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2699 helix: 1.41 (0.13), residues: 1524 sheet: -1.01 (0.33), residues: 227 loop : 0.11 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2825 HIS 0.005 0.001 HIS A2689 PHE 0.028 0.002 PHE A3513 TYR 0.018 0.001 TYR A2496 ARG 0.006 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.13619 ( 1257) hydrogen bonds : angle 5.85034 ( 3672) covalent geometry : bond 0.00393 (22340) covalent geometry : angle 0.68236 (30308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 266 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2263 HIS cc_start: 0.7263 (m90) cc_final: 0.6956 (m170) REVERT: A 2446 ILE cc_start: 0.8682 (tp) cc_final: 0.8446 (tt) outliers start: 13 outliers final: 1 residues processed: 272 average time/residue: 0.3318 time to fit residues: 144.6796 Evaluate side-chains 251 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1884 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 138 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 158 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 ASN A3197 GLN A3202 ASN A3622 ASN A4023 GLN A4466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098156 restraints weight = 45896.644| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.38 r_work: 0.3242 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22340 Z= 0.118 Angle : 0.555 11.733 30308 Z= 0.275 Chirality : 0.039 0.200 3412 Planarity : 0.004 0.064 3883 Dihedral : 7.026 164.723 3014 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.66 % Allowed : 15.04 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2699 helix: 1.80 (0.13), residues: 1531 sheet: -0.80 (0.33), residues: 229 loop : 0.18 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2825 HIS 0.008 0.001 HIS A2918 PHE 0.018 0.001 PHE A3996 TYR 0.018 0.001 TYR A2748 ARG 0.004 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1257) hydrogen bonds : angle 4.62827 ( 3672) covalent geometry : bond 0.00251 (22340) covalent geometry : angle 0.55487 (30308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1931 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8047 (p0) REVERT: A 1966 ARG cc_start: 0.8059 (ptp90) cc_final: 0.7818 (ttp-110) REVERT: A 2263 HIS cc_start: 0.7953 (m90) cc_final: 0.7722 (m170) REVERT: A 2281 THR cc_start: 0.9030 (m) cc_final: 0.8671 (p) REVERT: A 2615 MET cc_start: 0.6929 (mpp) cc_final: 0.6724 (mmt) REVERT: A 2767 GLU cc_start: 0.8563 (tt0) cc_final: 0.8032 (tm-30) REVERT: A 2851 ASP cc_start: 0.9103 (t0) cc_final: 0.8842 (t0) REVERT: A 2855 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A 3008 MET cc_start: 0.8737 (mmm) cc_final: 0.8455 (mmm) REVERT: A 3026 TYR cc_start: 0.5673 (t80) cc_final: 0.5461 (t80) REVERT: A 3030 MET cc_start: 0.6451 (mmm) cc_final: 0.6130 (mmm) REVERT: A 3500 MET cc_start: 0.8552 (tpp) cc_final: 0.8224 (tpp) REVERT: A 3972 TYR cc_start: 0.8373 (t80) cc_final: 0.8129 (t80) REVERT: A 4092 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7185 (mtt180) outliers start: 40 outliers final: 17 residues processed: 304 average time/residue: 0.3415 time to fit residues: 165.4462 Evaluate side-chains 266 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2389 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4489 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 139 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 193 optimal weight: 0.0570 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2932 HIS A3014 ASN A3584 ASN A4466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095063 restraints weight = 46004.268| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.29 r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22340 Z= 0.168 Angle : 0.559 12.097 30308 Z= 0.276 Chirality : 0.040 0.161 3412 Planarity : 0.004 0.051 3883 Dihedral : 7.016 177.164 3012 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.58 % Allowed : 14.87 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2699 helix: 1.84 (0.13), residues: 1534 sheet: -0.87 (0.33), residues: 241 loop : 0.21 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.006 0.001 HIS A2918 PHE 0.024 0.002 PHE A3496 TYR 0.017 0.001 TYR A2748 ARG 0.005 0.000 ARG A4400 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1257) hydrogen bonds : angle 4.46909 ( 3672) covalent geometry : bond 0.00390 (22340) covalent geometry : angle 0.55871 (30308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1931 ASN cc_start: 0.8479 (p0) cc_final: 0.8027 (p0) REVERT: A 1966 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7753 (ttp-110) REVERT: A 2263 HIS cc_start: 0.7941 (m90) cc_final: 0.7687 (m170) REVERT: A 2281 THR cc_start: 0.9074 (m) cc_final: 0.8715 (p) REVERT: A 2446 ILE cc_start: 0.8934 (tp) cc_final: 0.8597 (tt) REVERT: A 2767 GLU cc_start: 0.8629 (tt0) cc_final: 0.8109 (tm-30) REVERT: A 2851 ASP cc_start: 0.9126 (t0) cc_final: 0.8783 (t0) REVERT: A 2855 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 3001 ASP cc_start: 0.7222 (t0) cc_final: 0.6624 (p0) REVERT: A 3206 ARG cc_start: 0.4701 (OUTLIER) cc_final: 0.3990 (tpm-80) REVERT: A 3213 ASP cc_start: 0.2242 (OUTLIER) cc_final: 0.1273 (m-30) REVERT: A 3488 ARG cc_start: 0.4126 (OUTLIER) cc_final: 0.3227 (ttt180) REVERT: A 3500 MET cc_start: 0.8618 (tpp) cc_final: 0.8416 (tpp) REVERT: A 3654 ARG cc_start: 0.6546 (ptp90) cc_final: 0.6250 (ptt-90) REVERT: A 3972 TYR cc_start: 0.8380 (t80) cc_final: 0.8166 (t80) outliers start: 62 outliers final: 32 residues processed: 296 average time/residue: 0.4908 time to fit residues: 235.0272 Evaluate side-chains 276 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2389 GLU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3206 ARG Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3488 ARG Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 260 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A4453 ASN A4466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094299 restraints weight = 46862.460| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.35 r_work: 0.3178 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22340 Z= 0.158 Angle : 0.554 12.133 30308 Z= 0.271 Chirality : 0.040 0.184 3412 Planarity : 0.004 0.046 3883 Dihedral : 6.905 168.061 3012 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.16 % Allowed : 15.41 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.17), residues: 2699 helix: 1.86 (0.13), residues: 1535 sheet: -0.84 (0.33), residues: 241 loop : 0.23 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.005 0.001 HIS A2918 PHE 0.023 0.002 PHE A1658 TYR 0.016 0.001 TYR A2496 ARG 0.004 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1257) hydrogen bonds : angle 4.37026 ( 3672) covalent geometry : bond 0.00364 (22340) covalent geometry : angle 0.55445 (30308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 260 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1926 PHE cc_start: 0.7634 (t80) cc_final: 0.7332 (t80) REVERT: A 1931 ASN cc_start: 0.8530 (p0) cc_final: 0.8134 (p0) REVERT: A 2263 HIS cc_start: 0.7972 (m90) cc_final: 0.7712 (m170) REVERT: A 2281 THR cc_start: 0.9078 (m) cc_final: 0.8722 (p) REVERT: A 2438 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8556 (pt0) REVERT: A 2446 ILE cc_start: 0.8960 (tp) cc_final: 0.8603 (tt) REVERT: A 2686 MET cc_start: 0.7890 (mtm) cc_final: 0.7596 (mtm) REVERT: A 2767 GLU cc_start: 0.8643 (tt0) cc_final: 0.8124 (tm-30) REVERT: A 2851 ASP cc_start: 0.9105 (t0) cc_final: 0.8860 (t0) REVERT: A 2855 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 3008 MET cc_start: 0.8849 (mmm) cc_final: 0.8371 (mmp) REVERT: A 3026 TYR cc_start: 0.6088 (t80) cc_final: 0.5884 (t80) REVERT: A 3030 MET cc_start: 0.6749 (mmm) cc_final: 0.6393 (mmm) REVERT: A 3116 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 3213 ASP cc_start: 0.2110 (OUTLIER) cc_final: 0.1176 (m-30) REVERT: A 3488 ARG cc_start: 0.4136 (OUTLIER) cc_final: 0.3279 (ttt180) REVERT: A 3499 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: A 3654 ARG cc_start: 0.6699 (ptp90) cc_final: 0.6445 (ptt-90) REVERT: A 4025 LEU cc_start: 0.8400 (tt) cc_final: 0.8074 (tt) REVERT: A 4133 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8772 (ttmm) REVERT: A 4296 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7372 (tmm) outliers start: 76 outliers final: 42 residues processed: 312 average time/residue: 0.3489 time to fit residues: 172.9904 Evaluate side-chains 288 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2389 GLU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3488 ARG Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 229 optimal weight: 0.0980 chunk 128 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1779 HIS A3047 HIS A3800 GLN A4453 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.096308 restraints weight = 45999.328| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.33 r_work: 0.3212 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22340 Z= 0.111 Angle : 0.524 12.683 30308 Z= 0.255 Chirality : 0.038 0.178 3412 Planarity : 0.004 0.045 3883 Dihedral : 6.646 155.195 3012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.49 % Allowed : 16.54 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2699 helix: 2.02 (0.13), residues: 1536 sheet: -0.74 (0.33), residues: 241 loop : 0.27 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.005 0.001 HIS A2918 PHE 0.026 0.001 PHE A3496 TYR 0.017 0.001 TYR A3812 ARG 0.005 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1257) hydrogen bonds : angle 4.22687 ( 3672) covalent geometry : bond 0.00243 (22340) covalent geometry : angle 0.52426 (30308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1926 PHE cc_start: 0.7509 (t80) cc_final: 0.7257 (t80) REVERT: A 2263 HIS cc_start: 0.7925 (m90) cc_final: 0.7677 (m170) REVERT: A 2281 THR cc_start: 0.9007 (m) cc_final: 0.8655 (p) REVERT: A 2438 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8567 (pt0) REVERT: A 2446 ILE cc_start: 0.8963 (tp) cc_final: 0.8601 (tt) REVERT: A 2582 TYR cc_start: 0.8123 (t80) cc_final: 0.7731 (t80) REVERT: A 2767 GLU cc_start: 0.8606 (tt0) cc_final: 0.8114 (tm-30) REVERT: A 2851 ASP cc_start: 0.9126 (t0) cc_final: 0.8841 (t0) REVERT: A 2855 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 3008 MET cc_start: 0.8846 (mmm) cc_final: 0.8340 (mmp) REVERT: A 3116 GLU cc_start: 0.8137 (mm-30) cc_final: 0.6957 (mp0) REVERT: A 3213 ASP cc_start: 0.2176 (OUTLIER) cc_final: 0.1315 (m-30) REVERT: A 3488 ARG cc_start: 0.4111 (OUTLIER) cc_final: 0.3167 (ttt180) REVERT: A 3490 GLU cc_start: 0.7934 (pp20) cc_final: 0.7375 (pt0) REVERT: A 3524 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8783 (tpt) REVERT: A 3654 ARG cc_start: 0.6811 (ptp90) cc_final: 0.6601 (ptt180) REVERT: A 4133 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (ttmm) REVERT: A 4296 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7409 (tmm) outliers start: 60 outliers final: 32 residues processed: 308 average time/residue: 0.3610 time to fit residues: 177.0818 Evaluate side-chains 278 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2389 GLU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3488 ARG Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 6 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 211 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.095552 restraints weight = 46114.978| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.37 r_work: 0.3199 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22340 Z= 0.124 Angle : 0.531 13.278 30308 Z= 0.258 Chirality : 0.039 0.177 3412 Planarity : 0.004 0.043 3883 Dihedral : 6.513 144.609 3012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.78 % Allowed : 16.74 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2699 helix: 2.02 (0.13), residues: 1538 sheet: -0.83 (0.31), residues: 263 loop : 0.32 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A2658 HIS 0.004 0.001 HIS A2918 PHE 0.024 0.001 PHE A3496 TYR 0.016 0.001 TYR A2496 ARG 0.005 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1257) hydrogen bonds : angle 4.18966 ( 3672) covalent geometry : bond 0.00280 (22340) covalent geometry : angle 0.53089 (30308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1926 PHE cc_start: 0.7581 (t80) cc_final: 0.7346 (t80) REVERT: A 2263 HIS cc_start: 0.7935 (m90) cc_final: 0.7691 (m170) REVERT: A 2281 THR cc_start: 0.9009 (m) cc_final: 0.8650 (p) REVERT: A 2438 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8557 (pt0) REVERT: A 2446 ILE cc_start: 0.8993 (tp) cc_final: 0.8623 (tt) REVERT: A 2582 TYR cc_start: 0.8117 (t80) cc_final: 0.7746 (t80) REVERT: A 2767 GLU cc_start: 0.8607 (tt0) cc_final: 0.8105 (tm-30) REVERT: A 2851 ASP cc_start: 0.9134 (t0) cc_final: 0.8862 (t0) REVERT: A 2855 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 3008 MET cc_start: 0.8860 (mmm) cc_final: 0.8342 (mmp) REVERT: A 3116 GLU cc_start: 0.8118 (mm-30) cc_final: 0.6931 (mp0) REVERT: A 3213 ASP cc_start: 0.2103 (OUTLIER) cc_final: 0.1316 (m-30) REVERT: A 4133 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8754 (ttmm) REVERT: A 4296 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7527 (tmm) outliers start: 67 outliers final: 39 residues processed: 306 average time/residue: 0.4187 time to fit residues: 205.3932 Evaluate side-chains 284 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2389 GLU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 5 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 35 optimal weight: 0.0870 chunk 155 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.127316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096735 restraints weight = 46193.465| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.39 r_work: 0.3219 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22340 Z= 0.108 Angle : 0.532 12.152 30308 Z= 0.256 Chirality : 0.038 0.180 3412 Planarity : 0.004 0.042 3883 Dihedral : 6.311 136.414 3012 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.24 % Allowed : 17.66 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2699 helix: 2.07 (0.13), residues: 1539 sheet: -0.69 (0.32), residues: 253 loop : 0.31 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4387 HIS 0.004 0.001 HIS A2918 PHE 0.028 0.001 PHE A3496 TYR 0.016 0.001 TYR A3812 ARG 0.005 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1257) hydrogen bonds : angle 4.14448 ( 3672) covalent geometry : bond 0.00239 (22340) covalent geometry : angle 0.53217 (30308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1912 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8519 (mtmt) REVERT: A 1926 PHE cc_start: 0.7673 (t80) cc_final: 0.7450 (t80) REVERT: A 2018 MET cc_start: 0.8747 (mtp) cc_final: 0.8318 (mtm) REVERT: A 2263 HIS cc_start: 0.7921 (m90) cc_final: 0.7677 (m170) REVERT: A 2281 THR cc_start: 0.8965 (m) cc_final: 0.8606 (p) REVERT: A 2299 GLN cc_start: 0.7889 (mp10) cc_final: 0.7202 (mp10) REVERT: A 2438 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8543 (pt0) REVERT: A 2582 TYR cc_start: 0.8099 (t80) cc_final: 0.7872 (t80) REVERT: A 2767 GLU cc_start: 0.8588 (tt0) cc_final: 0.8091 (tm-30) REVERT: A 2851 ASP cc_start: 0.9097 (t0) cc_final: 0.8840 (t0) REVERT: A 2855 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 2994 MET cc_start: 0.8764 (mmm) cc_final: 0.8487 (mmm) REVERT: A 3008 MET cc_start: 0.8872 (mmm) cc_final: 0.8339 (mmp) REVERT: A 3016 GLU cc_start: 0.6931 (pp20) cc_final: 0.6693 (pp20) REVERT: A 3098 SER cc_start: 0.7627 (t) cc_final: 0.7304 (p) REVERT: A 3113 MET cc_start: 0.7068 (ptp) cc_final: 0.6552 (ptp) REVERT: A 3217 GLU cc_start: 0.2666 (OUTLIER) cc_final: 0.2239 (mp0) REVERT: A 4133 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (ttmm) REVERT: A 4296 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7490 (tmm) outliers start: 54 outliers final: 35 residues processed: 303 average time/residue: 0.3422 time to fit residues: 164.7090 Evaluate side-chains 284 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 131 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 264 optimal weight: 0.1980 chunk 167 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3014 ASN A4453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.127497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097003 restraints weight = 46297.124| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.39 r_work: 0.3221 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22340 Z= 0.110 Angle : 0.539 13.514 30308 Z= 0.260 Chirality : 0.038 0.188 3412 Planarity : 0.004 0.042 3883 Dihedral : 6.183 131.517 3012 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.08 % Allowed : 18.11 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2699 helix: 2.09 (0.13), residues: 1539 sheet: -0.71 (0.32), residues: 252 loop : 0.32 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A2658 HIS 0.006 0.001 HIS A1779 PHE 0.031 0.001 PHE A3496 TYR 0.016 0.001 TYR A2748 ARG 0.005 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 1257) hydrogen bonds : angle 4.12927 ( 3672) covalent geometry : bond 0.00242 (22340) covalent geometry : angle 0.53875 (30308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1912 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8516 (mtmm) REVERT: A 1926 PHE cc_start: 0.7685 (t80) cc_final: 0.7456 (t80) REVERT: A 2018 MET cc_start: 0.8771 (mtp) cc_final: 0.8367 (mtm) REVERT: A 2263 HIS cc_start: 0.7924 (m90) cc_final: 0.7677 (m170) REVERT: A 2281 THR cc_start: 0.8953 (m) cc_final: 0.8595 (p) REVERT: A 2299 GLN cc_start: 0.7899 (mp10) cc_final: 0.7214 (mp10) REVERT: A 2302 VAL cc_start: 0.9004 (t) cc_final: 0.8778 (m) REVERT: A 2438 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8544 (pt0) REVERT: A 2582 TYR cc_start: 0.8048 (t80) cc_final: 0.7831 (t80) REVERT: A 2767 GLU cc_start: 0.8603 (tt0) cc_final: 0.8109 (tm-30) REVERT: A 2851 ASP cc_start: 0.9140 (t0) cc_final: 0.8853 (t0) REVERT: A 2855 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 3008 MET cc_start: 0.8875 (mmm) cc_final: 0.8326 (mmp) REVERT: A 3016 GLU cc_start: 0.6891 (pp20) cc_final: 0.6644 (pp20) REVERT: A 3113 MET cc_start: 0.7179 (ptp) cc_final: 0.6656 (ptp) REVERT: A 3116 GLU cc_start: 0.8180 (mm-30) cc_final: 0.6950 (mp0) REVERT: A 3213 ASP cc_start: 0.2310 (OUTLIER) cc_final: 0.1942 (m-30) REVERT: A 3217 GLU cc_start: 0.2715 (OUTLIER) cc_final: 0.2477 (mt-10) REVERT: A 4133 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (ttmm) REVERT: A 4296 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7495 (tmm) outliers start: 50 outliers final: 36 residues processed: 292 average time/residue: 0.3404 time to fit residues: 158.8125 Evaluate side-chains 286 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4466 HIS Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2789 GLN A3014 ASN A3622 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097282 restraints weight = 46218.867| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.39 r_work: 0.3227 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22340 Z= 0.109 Angle : 0.534 13.654 30308 Z= 0.259 Chirality : 0.038 0.195 3412 Planarity : 0.004 0.042 3883 Dihedral : 6.063 127.502 3012 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.12 % Allowed : 18.03 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.17), residues: 2699 helix: 2.11 (0.13), residues: 1541 sheet: -0.56 (0.32), residues: 242 loop : 0.23 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2658 HIS 0.005 0.001 HIS A1779 PHE 0.030 0.001 PHE A3496 TYR 0.019 0.001 TYR A4447 ARG 0.003 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1257) hydrogen bonds : angle 4.12121 ( 3672) covalent geometry : bond 0.00240 (22340) covalent geometry : angle 0.53409 (30308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1926 PHE cc_start: 0.7704 (t80) cc_final: 0.7474 (t80) REVERT: A 2018 MET cc_start: 0.8784 (mtp) cc_final: 0.8352 (mtm) REVERT: A 2263 HIS cc_start: 0.7953 (m90) cc_final: 0.7690 (m170) REVERT: A 2281 THR cc_start: 0.8936 (m) cc_final: 0.8580 (p) REVERT: A 2299 GLN cc_start: 0.7919 (mp10) cc_final: 0.7230 (mp10) REVERT: A 2438 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8529 (pt0) REVERT: A 2446 ILE cc_start: 0.8840 (tp) cc_final: 0.8588 (tt) REVERT: A 2522 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8128 (t) REVERT: A 2582 TYR cc_start: 0.8024 (t80) cc_final: 0.7710 (t80) REVERT: A 2767 GLU cc_start: 0.8602 (tt0) cc_final: 0.8107 (tm-30) REVERT: A 2851 ASP cc_start: 0.9146 (t0) cc_final: 0.8843 (t0) REVERT: A 2855 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 3008 MET cc_start: 0.8888 (mmm) cc_final: 0.8335 (mmp) REVERT: A 3016 GLU cc_start: 0.6902 (pp20) cc_final: 0.6654 (pp20) REVERT: A 3098 SER cc_start: 0.7614 (t) cc_final: 0.7391 (m) REVERT: A 3113 MET cc_start: 0.7208 (ptp) cc_final: 0.6741 (ptp) REVERT: A 3116 GLU cc_start: 0.8149 (mm-30) cc_final: 0.6923 (mp0) REVERT: A 3213 ASP cc_start: 0.2278 (OUTLIER) cc_final: 0.1942 (m-30) REVERT: A 3217 GLU cc_start: 0.2609 (OUTLIER) cc_final: 0.2281 (mp0) REVERT: A 4133 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (ttmm) REVERT: A 4296 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7520 (tmm) outliers start: 51 outliers final: 38 residues processed: 293 average time/residue: 0.3584 time to fit residues: 169.3655 Evaluate side-chains 288 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2884 VAL Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3876 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4466 HIS Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3014 ASN A3047 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.126713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096213 restraints weight = 46344.217| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.39 r_work: 0.3210 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22340 Z= 0.131 Angle : 0.570 13.730 30308 Z= 0.278 Chirality : 0.039 0.204 3412 Planarity : 0.004 0.041 3883 Dihedral : 6.099 133.763 3012 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.87 % Allowed : 18.40 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2699 helix: 2.10 (0.13), residues: 1540 sheet: -0.63 (0.32), residues: 252 loop : 0.25 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2658 HIS 0.005 0.001 HIS A1779 PHE 0.031 0.001 PHE A3496 TYR 0.016 0.001 TYR A3812 ARG 0.007 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1257) hydrogen bonds : angle 4.12968 ( 3672) covalent geometry : bond 0.00301 (22340) covalent geometry : angle 0.57003 (30308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1926 PHE cc_start: 0.7716 (t80) cc_final: 0.7492 (t80) REVERT: A 2018 MET cc_start: 0.8795 (mtp) cc_final: 0.8382 (mtm) REVERT: A 2263 HIS cc_start: 0.7930 (m90) cc_final: 0.7685 (m170) REVERT: A 2281 THR cc_start: 0.8948 (m) cc_final: 0.8588 (p) REVERT: A 2299 GLN cc_start: 0.7955 (mp10) cc_final: 0.7306 (mp10) REVERT: A 2438 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8543 (pt0) REVERT: A 2446 ILE cc_start: 0.8884 (tp) cc_final: 0.8640 (tt) REVERT: A 2522 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 2582 TYR cc_start: 0.8037 (t80) cc_final: 0.7719 (t80) REVERT: A 2767 GLU cc_start: 0.8616 (tt0) cc_final: 0.8117 (tm-30) REVERT: A 2851 ASP cc_start: 0.9129 (t0) cc_final: 0.8868 (t0) REVERT: A 2855 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 3008 MET cc_start: 0.8882 (mmm) cc_final: 0.8316 (mmp) REVERT: A 3016 GLU cc_start: 0.7025 (pp20) cc_final: 0.6700 (pp20) REVERT: A 3113 MET cc_start: 0.7366 (ptp) cc_final: 0.6869 (ptp) REVERT: A 3116 GLU cc_start: 0.8221 (mm-30) cc_final: 0.6989 (mp0) REVERT: A 3213 ASP cc_start: 0.2224 (OUTLIER) cc_final: 0.1899 (m-30) REVERT: A 3217 GLU cc_start: 0.2735 (OUTLIER) cc_final: 0.2427 (mp0) REVERT: A 3488 ARG cc_start: 0.4210 (OUTLIER) cc_final: 0.3921 (ttp80) REVERT: A 3652 GLU cc_start: 0.8167 (pp20) cc_final: 0.7918 (mt-10) REVERT: A 4296 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: A 4377 MET cc_start: 0.8458 (tmm) cc_final: 0.8114 (tpp) outliers start: 45 outliers final: 36 residues processed: 280 average time/residue: 0.3448 time to fit residues: 153.6849 Evaluate side-chains 286 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2884 VAL Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3488 ARG Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3876 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4489 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 0.0000 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3014 ASN A4453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096021 restraints weight = 46371.497| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.39 r_work: 0.3206 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22340 Z= 0.132 Angle : 0.578 12.925 30308 Z= 0.282 Chirality : 0.039 0.211 3412 Planarity : 0.004 0.065 3883 Dihedral : 6.108 132.781 3012 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.95 % Allowed : 18.57 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2699 helix: 2.10 (0.13), residues: 1531 sheet: -0.61 (0.31), residues: 267 loop : 0.31 (0.22), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A2658 HIS 0.005 0.001 HIS A1779 PHE 0.031 0.002 PHE A3496 TYR 0.021 0.001 TYR A3026 ARG 0.026 0.000 ARG A2843 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1257) hydrogen bonds : angle 4.15684 ( 3672) covalent geometry : bond 0.00304 (22340) covalent geometry : angle 0.57822 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12107.58 seconds wall clock time: 214 minutes 18.20 seconds (12858.20 seconds total)