Starting phenix.real_space_refine on Fri Sep 19 02:16:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmn_44704/09_2025/9bmn_44704.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.29, per 1000 atoms: 0.24 Number of scatterers: 21867 At special positions: 0 Unit cell: (148.428, 160.146, 119.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4078 8.00 N 3777 7.00 C 13892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 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: 1.32 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 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: 4.276A 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: 3.509A 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: 3.557A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.505A 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: 3.693A 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: 4.120A 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: 5.140A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.041A 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: 3.761A 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: 4.441A 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: 3.912A 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: 3.603A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.944A 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: 3.770A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.244A 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: 3.940A 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: 5.601A 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: 6.209A 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: 3.972A 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: 6.228A 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: 6.542A 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: 6.355A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.320A 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: 8.334A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 2.67 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: 6178 1.33 - 1.46: 4170 1.46 - 1.58: 11792 1.58 - 1.70: 15 1.70 - 1.82: 185 Bond restraints: 22340 Sorted by residual: bond pdb=" CB PRO A1848 " pdb=" CG PRO A1848 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.03e+00 bond pdb=" CB PRO A2812 " pdb=" CG PRO A2812 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.73e+00 bond pdb=" CB PRO A2020 " pdb=" CG PRO A2020 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.68e+00 bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.331 1.355 -0.024 1.27e-02 6.20e+03 3.67e+00 bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 22335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 30027 2.76 - 5.51: 248 5.51 - 8.27: 21 8.27 - 11.03: 9 11.03 - 13.79: 3 Bond angle restraints: 30308 Sorted by residual: 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=" CA PRO A1848 " pdb=" N PRO A1848 " pdb=" CD PRO A1848 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" CA PRO A2020 " pdb=" N PRO A2020 " pdb=" CD PRO A2020 " ideal model delta sigma weight residual 112.00 104.98 7.02 1.40e+00 5.10e-01 2.52e+01 angle pdb=" CA MET A3791 " pdb=" CB MET A3791 " pdb=" CG MET A3791 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA LEU A4311 " pdb=" CB LEU A4311 " pdb=" CG LEU A4311 " ideal model delta sigma weight residual 116.30 130.09 -13.79 3.50e+00 8.16e-02 1.55e+01 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 12866 30.27 - 60.53: 614 60.53 - 90.80: 60 90.80 - 121.06: 1 121.06 - 151.33: 1 Dihedral angle restraints: 13542 sinusoidal: 5612 harmonic: 7930 Sorted by residual: dihedral pdb=" C2' ADP A4701 " pdb=" C1' ADP A4701 " pdb=" N9 ADP A4701 " pdb=" C4 ADP A4701 " ideal model delta sinusoidal sigma weight residual 91.55 -117.12 -151.33 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 41.90 -101.90 1 2.00e+01 2.50e-03 2.89e+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 -60.00 22.46 -82.45 1 2.00e+01 2.50e-03 2.08e+01 ... (remaining 13539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2829 0.050 - 0.100: 493 0.100 - 0.150: 88 0.150 - 0.201: 1 0.201 - 0.251: 1 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 1.57e+00 chirality pdb=" CA GLN A3499 " pdb=" N GLN A3499 " pdb=" C GLN A3499 " pdb=" CB GLN A3499 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE A2882 " pdb=" N ILE A2882 " pdb=" C ILE A2882 " pdb=" CB ILE A2882 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (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 2.18e+01 pdb=" N PRO A1848 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO A1848 " -0.058 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: 604 2.71 - 3.26: 23439 3.26 - 3.81: 37140 3.81 - 4.35: 45413 4.35 - 4.90: 75168 Nonbonded interactions: 181764 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=" OG1 THR A1913 " pdb=" O1A ADP A4701 " model vdw 2.201 3.040 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 ... (remaining 181759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.123 22340 Z= 0.155 Angle : 0.647 13.787 30308 Z= 0.336 Chirality : 0.040 0.251 3412 Planarity : 0.005 0.132 3883 Dihedral : 16.536 151.329 8390 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.25 % Allowed : 16.41 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.17), residues: 2699 helix: 1.53 (0.13), residues: 1525 sheet: -1.01 (0.33), residues: 227 loop : 0.15 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1966 TYR 0.017 0.001 TYR A3812 PHE 0.028 0.002 PHE A3513 TRP 0.023 0.001 TRP A2825 HIS 0.005 0.001 HIS A2689 Details of bonding type rmsd covalent geometry : bond 0.00356 (22340) covalent geometry : angle 0.64721 (30308) hydrogen bonds : bond 0.13539 ( 1258) hydrogen bonds : angle 5.75988 ( 3675) *********************** 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 675 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 669 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1795 SER cc_start: 0.9051 (m) cc_final: 0.8577 (t) REVERT: A 1879 LEU cc_start: 0.7248 (tp) cc_final: 0.5780 (tp) REVERT: A 1892 MET cc_start: 0.8691 (mmt) cc_final: 0.8362 (mmm) REVERT: A 1959 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 2012 MET cc_start: 0.8802 (tpp) cc_final: 0.8510 (tpp) REVERT: A 2084 SER cc_start: 0.8867 (m) cc_final: 0.8586 (p) REVERT: A 2097 LEU cc_start: 0.9304 (mm) cc_final: 0.9034 (mt) REVERT: A 2099 SER cc_start: 0.9153 (m) cc_final: 0.8683 (p) REVERT: A 2279 LEU cc_start: 0.8358 (tp) cc_final: 0.7627 (tp) REVERT: A 2659 LEU cc_start: 0.8085 (tp) cc_final: 0.7833 (tt) REVERT: A 2779 MET cc_start: 0.7562 (ptp) cc_final: 0.7248 (ptp) REVERT: A 2980 LEU cc_start: 0.9302 (mm) cc_final: 0.9072 (mm) REVERT: A 3030 MET cc_start: 0.6938 (mmm) cc_final: 0.5708 (tpt) REVERT: A 3076 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8454 (mtpp) REVERT: A 3199 MET cc_start: 0.7289 (mtp) cc_final: 0.7039 (tmm) REVERT: A 3586 TYR cc_start: 0.7798 (m-80) cc_final: 0.7552 (m-10) REVERT: A 3683 ASP cc_start: 0.8600 (t0) cc_final: 0.8311 (t0) REVERT: A 4055 VAL cc_start: 0.9134 (p) cc_final: 0.8813 (p) REVERT: A 4124 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7332 (tp) REVERT: A 4247 MET cc_start: 0.8453 (mtm) cc_final: 0.8202 (mtm) REVERT: A 4604 VAL cc_start: 0.8030 (t) cc_final: 0.7686 (p) REVERT: A 4626 ILE cc_start: 0.8408 (pt) cc_final: 0.7790 (pt) outliers start: 6 outliers final: 0 residues processed: 672 average time/residue: 0.1950 time to fit residues: 193.8760 Evaluate side-chains 362 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4124 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** A1979 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2725 HIS ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN A3119 ASN A3197 GLN A3202 ASN A3535 HIS A3584 ASN A3622 ASN A3800 GLN A3838 ASN A3907 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.109538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083065 restraints weight = 64034.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085675 restraints weight = 34907.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087364 restraints weight = 24099.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088475 restraints weight = 19215.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089126 restraints weight = 16687.215| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22340 Z= 0.177 Angle : 0.667 9.846 30308 Z= 0.331 Chirality : 0.042 0.191 3412 Planarity : 0.005 0.072 3883 Dihedral : 7.169 153.753 3014 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.70 % Allowed : 18.57 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.16), residues: 2699 helix: 1.68 (0.13), residues: 1536 sheet: -1.08 (0.33), residues: 231 loop : 0.21 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3728 TYR 0.025 0.002 TYR A1872 PHE 0.023 0.002 PHE A4613 TRP 0.018 0.002 TRP A2825 HIS 0.008 0.001 HIS A2725 Details of bonding type rmsd covalent geometry : bond 0.00396 (22340) covalent geometry : angle 0.66722 (30308) hydrogen bonds : bond 0.04500 ( 1258) hydrogen bonds : angle 4.79129 ( 3675) *********************** 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 428 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 363 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6468 (tpt) cc_final: 0.5943 (mtp) REVERT: A 1892 MET cc_start: 0.9199 (mmt) cc_final: 0.8868 (mmm) REVERT: A 1958 ASP cc_start: 0.8299 (t0) cc_final: 0.8018 (t0) REVERT: A 1959 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6903 (mm-30) REVERT: A 2012 MET cc_start: 0.8989 (tpp) cc_final: 0.8565 (tpp) REVERT: A 2018 MET cc_start: 0.7376 (mtm) cc_final: 0.7125 (mtt) REVERT: A 2033 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8943 (mmtt) REVERT: A 2084 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 2099 SER cc_start: 0.9484 (m) cc_final: 0.9011 (p) REVERT: A 2133 GLU cc_start: 0.8122 (pm20) cc_final: 0.7885 (pm20) REVERT: A 2273 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5984 (ttp80) REVERT: A 2284 LEU cc_start: 0.8636 (mt) cc_final: 0.8434 (mt) REVERT: A 2510 MET cc_start: 0.8188 (mpp) cc_final: 0.7714 (ptp) REVERT: A 2659 LEU cc_start: 0.8275 (tp) cc_final: 0.7863 (tt) REVERT: A 2847 ASP cc_start: 0.9031 (m-30) cc_final: 0.8734 (m-30) REVERT: A 2888 GLU cc_start: 0.8328 (mp0) cc_final: 0.8114 (pm20) REVERT: A 2962 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7639 (pptt) REVERT: A 2980 LEU cc_start: 0.9440 (mm) cc_final: 0.9204 (mm) REVERT: A 3030 MET cc_start: 0.7324 (mmm) cc_final: 0.6856 (mmp) REVERT: A 3078 ARG cc_start: 0.8807 (mmp80) cc_final: 0.8051 (mmp80) REVERT: A 3199 MET cc_start: 0.7096 (mtp) cc_final: 0.6811 (tmm) REVERT: A 3506 ASP cc_start: 0.6929 (m-30) cc_final: 0.6481 (m-30) REVERT: A 3586 TYR cc_start: 0.8241 (m-80) cc_final: 0.7746 (m-10) REVERT: A 3591 ASP cc_start: 0.7252 (t0) cc_final: 0.6421 (p0) REVERT: A 3683 ASP cc_start: 0.8788 (t0) cc_final: 0.8336 (t0) REVERT: A 3815 MET cc_start: 0.8436 (mtp) cc_final: 0.8136 (mtp) REVERT: A 3873 ARG cc_start: 0.8325 (mmt180) cc_final: 0.8003 (mmm160) REVERT: A 3960 TRP cc_start: 0.8396 (t60) cc_final: 0.7527 (t60) REVERT: A 4195 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8069 (mtm110) REVERT: A 4296 MET cc_start: 0.9003 (tmm) cc_final: 0.8455 (tmm) REVERT: A 4377 MET cc_start: 0.6424 (tmm) cc_final: 0.5839 (ppp) REVERT: A 4604 VAL cc_start: 0.8486 (t) cc_final: 0.8060 (p) outliers start: 65 outliers final: 30 residues processed: 406 average time/residue: 0.1729 time to fit residues: 107.7690 Evaluate side-chains 327 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 1943 ARG Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 38 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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** A1863 ASN A1979 GLN A2482 GLN A3032 GLN A3538 GLN ** A3799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3906 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080835 restraints weight = 64109.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083366 restraints weight = 34768.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085016 restraints weight = 23891.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086051 restraints weight = 18933.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086567 restraints weight = 16431.963| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22340 Z= 0.192 Angle : 0.645 9.297 30308 Z= 0.317 Chirality : 0.042 0.331 3412 Planarity : 0.005 0.058 3883 Dihedral : 6.932 152.939 3012 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.20 % Allowed : 19.86 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.16), residues: 2699 helix: 1.67 (0.13), residues: 1538 sheet: -1.15 (0.33), residues: 224 loop : 0.20 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2467 TYR 0.018 0.002 TYR A2496 PHE 0.025 0.002 PHE A4613 TRP 0.015 0.001 TRP A2825 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00437 (22340) covalent geometry : angle 0.64525 (30308) hydrogen bonds : bond 0.04298 ( 1258) hydrogen bonds : angle 4.65137 ( 3675) *********************** 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 371 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 294 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.9192 (mmt) cc_final: 0.8852 (mmm) REVERT: A 1937 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 1938 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 1958 ASP cc_start: 0.8472 (t0) cc_final: 0.8172 (t0) REVERT: A 1959 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 2012 MET cc_start: 0.8909 (tpp) cc_final: 0.8618 (tpp) REVERT: A 2084 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 2099 SER cc_start: 0.9466 (m) cc_final: 0.9033 (p) REVERT: A 2130 ASN cc_start: 0.8818 (m110) cc_final: 0.8534 (p0) REVERT: A 2157 LEU cc_start: 0.9097 (tp) cc_final: 0.8878 (tt) REVERT: A 2273 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6587 (ttp80) REVERT: A 2467 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8259 (mtm110) REVERT: A 2510 MET cc_start: 0.8185 (mpp) cc_final: 0.7788 (ptp) REVERT: A 2659 LEU cc_start: 0.8375 (tp) cc_final: 0.7938 (tt) REVERT: A 2717 ASP cc_start: 0.7272 (t70) cc_final: 0.6949 (p0) REVERT: A 2799 MET cc_start: 0.6778 (mmm) cc_final: 0.6535 (ttm) REVERT: A 2847 ASP cc_start: 0.9041 (m-30) cc_final: 0.8721 (m-30) REVERT: A 2888 GLU cc_start: 0.8307 (mp0) cc_final: 0.8021 (pm20) REVERT: A 2962 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7709 (pptt) REVERT: A 2967 TYR cc_start: 0.7356 (t80) cc_final: 0.7133 (t80) REVERT: A 2994 MET cc_start: 0.8039 (mmm) cc_final: 0.7053 (tpp) REVERT: A 3030 MET cc_start: 0.7459 (mmm) cc_final: 0.7040 (mmm) REVERT: A 3078 ARG cc_start: 0.8777 (mmp80) cc_final: 0.8249 (mmp80) REVERT: A 3169 MET cc_start: 0.7449 (mmm) cc_final: 0.7244 (mmm) REVERT: A 3199 MET cc_start: 0.7046 (mtp) cc_final: 0.6826 (tmm) REVERT: A 3500 MET cc_start: 0.8098 (mmm) cc_final: 0.7563 (mmm) REVERT: A 3547 ILE cc_start: 0.6714 (tp) cc_final: 0.6412 (tp) REVERT: A 3586 TYR cc_start: 0.8289 (m-80) cc_final: 0.7596 (m-10) REVERT: A 3591 ASP cc_start: 0.7515 (t0) cc_final: 0.6487 (p0) REVERT: A 3683 ASP cc_start: 0.8854 (t0) cc_final: 0.8358 (t0) REVERT: A 3873 ARG cc_start: 0.8372 (mmt180) cc_final: 0.7926 (mmm160) REVERT: A 3960 TRP cc_start: 0.8460 (t60) cc_final: 0.8110 (t60) REVERT: A 4195 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8140 (mtm110) REVERT: A 4296 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8490 (tmm) REVERT: A 4377 MET cc_start: 0.6332 (tmm) cc_final: 0.5701 (ppp) REVERT: A 4422 LYS cc_start: 0.8667 (tmmt) cc_final: 0.8411 (tmmt) REVERT: A 4604 VAL cc_start: 0.8621 (t) cc_final: 0.8224 (p) outliers start: 77 outliers final: 44 residues processed: 342 average time/residue: 0.1558 time to fit residues: 83.1288 Evaluate side-chains 317 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 267 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 1943 ARG Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 1979 GLN Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2467 ARG Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 3 optimal weight: 20.0000 chunk 116 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2789 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.106256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080653 restraints weight = 63694.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083151 restraints weight = 34381.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084798 restraints weight = 23515.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085870 restraints weight = 18528.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086521 restraints weight = 15994.073| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22340 Z= 0.161 Angle : 0.611 8.945 30308 Z= 0.299 Chirality : 0.041 0.279 3412 Planarity : 0.004 0.052 3883 Dihedral : 6.600 153.980 3012 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.20 % Allowed : 19.73 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.16), residues: 2699 helix: 1.77 (0.13), residues: 1539 sheet: -1.09 (0.33), residues: 217 loop : 0.19 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2358 TYR 0.021 0.001 TYR A2496 PHE 0.024 0.002 PHE A2036 TRP 0.018 0.001 TRP A4105 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00362 (22340) covalent geometry : angle 0.61117 (30308) hydrogen bonds : bond 0.04063 ( 1258) hydrogen bonds : angle 4.53479 ( 3675) *********************** 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 361 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 284 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.9194 (mmt) cc_final: 0.8889 (mmm) REVERT: A 1937 ASP cc_start: 0.8606 (p0) cc_final: 0.7528 (p0) REVERT: A 1938 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 1958 ASP cc_start: 0.8503 (t0) cc_final: 0.7899 (m-30) REVERT: A 1959 GLU cc_start: 0.7759 (mm-30) cc_final: 0.6928 (mm-30) REVERT: A 1960 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 2012 MET cc_start: 0.8871 (tpp) cc_final: 0.8640 (tpp) REVERT: A 2084 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8545 (p) REVERT: A 2099 SER cc_start: 0.9466 (m) cc_final: 0.9033 (p) REVERT: A 2130 ASN cc_start: 0.8783 (m110) cc_final: 0.8578 (p0) REVERT: A 2157 LEU cc_start: 0.9074 (tp) cc_final: 0.8829 (tt) REVERT: A 2273 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6540 (ttp80) REVERT: A 2499 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8723 (mm) REVERT: A 2510 MET cc_start: 0.8233 (mpp) cc_final: 0.7583 (mtt) REVERT: A 2717 ASP cc_start: 0.7296 (t70) cc_final: 0.6951 (p0) REVERT: A 2847 ASP cc_start: 0.9005 (m-30) cc_final: 0.8700 (m-30) REVERT: A 2914 GLU cc_start: 0.8300 (mp0) cc_final: 0.8083 (mp0) REVERT: A 2962 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7646 (pptt) REVERT: A 2967 TYR cc_start: 0.7216 (t80) cc_final: 0.7012 (t80) REVERT: A 2994 MET cc_start: 0.8218 (mmm) cc_final: 0.7403 (tpp) REVERT: A 3030 MET cc_start: 0.7943 (mmm) cc_final: 0.7440 (mmm) REVERT: A 3078 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8265 (mmp80) REVERT: A 3199 MET cc_start: 0.6920 (mtp) cc_final: 0.6720 (tmm) REVERT: A 3547 ILE cc_start: 0.6860 (tp) cc_final: 0.6563 (tp) REVERT: A 3586 TYR cc_start: 0.8370 (m-80) cc_final: 0.8022 (m-10) REVERT: A 3591 ASP cc_start: 0.7620 (t0) cc_final: 0.6513 (p0) REVERT: A 3819 LYS cc_start: 0.9323 (ttpp) cc_final: 0.9102 (ttpp) REVERT: A 3873 ARG cc_start: 0.8405 (mmt180) cc_final: 0.8019 (mmm160) REVERT: A 4296 MET cc_start: 0.9136 (tmm) cc_final: 0.8530 (tmm) REVERT: A 4462 ARG cc_start: 0.7394 (tpp80) cc_final: 0.7162 (tpp80) REVERT: A 4604 VAL cc_start: 0.8679 (t) cc_final: 0.8295 (p) outliers start: 77 outliers final: 45 residues processed: 337 average time/residue: 0.1507 time to fit residues: 80.2583 Evaluate side-chains 310 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 1943 ARG Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4272 LEU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 250 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** A1979 GLN A2752 ASN A3087 ASN ** A3636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.110424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086313 restraints weight = 66341.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089223 restraints weight = 34347.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089611 restraints weight = 21658.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089791 restraints weight = 20510.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089936 restraints weight = 18460.959| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4140 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= 0.151 Angle : 0.603 10.482 30308 Z= 0.294 Chirality : 0.041 0.340 3412 Planarity : 0.004 0.055 3883 Dihedral : 6.302 155.731 3012 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.61 % Allowed : 20.02 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.16), residues: 2699 helix: 1.81 (0.13), residues: 1540 sheet: -1.11 (0.34), residues: 203 loop : 0.20 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2358 TYR 0.020 0.001 TYR A2496 PHE 0.019 0.002 PHE A4613 TRP 0.014 0.001 TRP A2825 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00340 (22340) covalent geometry : angle 0.60319 (30308) hydrogen bonds : bond 0.03896 ( 1258) hydrogen bonds : angle 4.44960 ( 3675) *********************** 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 372 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5664 (mmm) cc_final: 0.4918 (mmm) REVERT: A 1892 MET cc_start: 0.9058 (mmt) cc_final: 0.8795 (mmm) REVERT: A 1937 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7525 (p0) REVERT: A 1938 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7499 (t80) REVERT: A 1958 ASP cc_start: 0.8444 (t0) cc_final: 0.7879 (m-30) REVERT: A 1959 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6855 (tp30) REVERT: A 1960 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 1979 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8085 (tp40) REVERT: A 2084 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 2099 SER cc_start: 0.9441 (m) cc_final: 0.8978 (p) REVERT: A 2149 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 2273 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6636 (ttp80) REVERT: A 2302 VAL cc_start: 0.9114 (t) cc_final: 0.8862 (m) REVERT: A 2499 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 2510 MET cc_start: 0.8154 (mpp) cc_final: 0.7564 (mtt) REVERT: A 2635 PHE cc_start: 0.8712 (m-80) cc_final: 0.8501 (m-80) REVERT: A 2717 ASP cc_start: 0.7185 (t70) cc_final: 0.6958 (p0) REVERT: A 2847 ASP cc_start: 0.8914 (m-30) cc_final: 0.8629 (m-30) REVERT: A 2962 LYS cc_start: 0.8478 (mmtt) cc_final: 0.7618 (pptt) REVERT: A 2994 MET cc_start: 0.8222 (mmm) cc_final: 0.7705 (tpp) REVERT: A 3030 MET cc_start: 0.7975 (mmm) cc_final: 0.7473 (mmm) REVERT: A 3199 MET cc_start: 0.7075 (mtp) cc_final: 0.6808 (tmm) REVERT: A 3208 ILE cc_start: 0.4830 (OUTLIER) cc_final: 0.4618 (mp) REVERT: A 3547 ILE cc_start: 0.6911 (tp) cc_final: 0.6667 (tp) REVERT: A 3586 TYR cc_start: 0.8309 (m-80) cc_final: 0.8099 (m-10) REVERT: A 3591 ASP cc_start: 0.7599 (t0) cc_final: 0.6491 (p0) REVERT: A 3819 LYS cc_start: 0.9266 (ttpp) cc_final: 0.9064 (ttpp) REVERT: A 3873 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7911 (mmm160) REVERT: A 3960 TRP cc_start: 0.8449 (t60) cc_final: 0.7789 (t60) REVERT: A 3991 LEU cc_start: 0.9224 (mt) cc_final: 0.8870 (mt) REVERT: A 4296 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8680 (tmm) REVERT: A 4346 MET cc_start: 0.8866 (mmp) cc_final: 0.8641 (mmm) REVERT: A 4462 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7353 (tpp80) REVERT: A 4604 VAL cc_start: 0.8598 (t) cc_final: 0.8233 (p) outliers start: 87 outliers final: 57 residues processed: 347 average time/residue: 0.1479 time to fit residues: 81.9853 Evaluate side-chains 329 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 1943 ARG Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 1979 GLN Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4272 LEU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4614 THR Chi-restraints excluded: chain A residue 4618 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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** A1979 GLN A2707 GLN ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.110649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.085794 restraints weight = 64394.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088421 restraints weight = 33750.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.090065 restraints weight = 22803.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091203 restraints weight = 18034.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091862 restraints weight = 15502.175| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22340 Z= 0.119 Angle : 0.604 10.045 30308 Z= 0.291 Chirality : 0.040 0.294 3412 Planarity : 0.004 0.051 3883 Dihedral : 6.209 157.244 3012 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.24 % Allowed : 20.65 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.16), residues: 2699 helix: 1.91 (0.13), residues: 1535 sheet: -1.05 (0.34), residues: 203 loop : 0.22 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2358 TYR 0.022 0.001 TYR A2496 PHE 0.019 0.001 PHE A1870 TRP 0.012 0.001 TRP A2825 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00262 (22340) covalent geometry : angle 0.60448 (30308) hydrogen bonds : bond 0.03731 ( 1258) hydrogen bonds : angle 4.35368 ( 3675) *********************** 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 370 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 292 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.9181 (mmt) cc_final: 0.8899 (mmm) REVERT: A 1937 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7356 (p0) REVERT: A 1938 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7558 (t80) REVERT: A 1958 ASP cc_start: 0.8369 (t0) cc_final: 0.7798 (m-30) REVERT: A 1959 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6005 (tt0) REVERT: A 1960 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 2099 SER cc_start: 0.9445 (m) cc_final: 0.8975 (p) REVERT: A 2510 MET cc_start: 0.8183 (mpp) cc_final: 0.7694 (mtt) REVERT: A 2615 MET cc_start: 0.7052 (ppp) cc_final: 0.6686 (ppp) REVERT: A 2635 PHE cc_start: 0.8793 (m-80) cc_final: 0.8505 (m-80) REVERT: A 2704 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 2717 ASP cc_start: 0.7211 (t70) cc_final: 0.6963 (p0) REVERT: A 2847 ASP cc_start: 0.8882 (m-30) cc_final: 0.8618 (m-30) REVERT: A 2962 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7699 (pptt) REVERT: A 2973 ASP cc_start: 0.8293 (p0) cc_final: 0.7782 (p0) REVERT: A 2994 MET cc_start: 0.8133 (mmm) cc_final: 0.7786 (tpp) REVERT: A 3030 MET cc_start: 0.7814 (mmm) cc_final: 0.7383 (mmm) REVERT: A 3199 MET cc_start: 0.7138 (mtp) cc_final: 0.6899 (tmm) REVERT: A 3208 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4591 (mp) REVERT: A 3547 ILE cc_start: 0.6894 (tp) cc_final: 0.6553 (tp) REVERT: A 3586 TYR cc_start: 0.8442 (m-80) cc_final: 0.8128 (m-10) REVERT: A 3591 ASP cc_start: 0.7522 (t0) cc_final: 0.6632 (p0) REVERT: A 3819 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8989 (ttpp) REVERT: A 3873 ARG cc_start: 0.8315 (mmt180) cc_final: 0.7910 (mmm160) REVERT: A 3933 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 3960 TRP cc_start: 0.8365 (t60) cc_final: 0.7725 (t60) REVERT: A 3991 LEU cc_start: 0.9182 (mt) cc_final: 0.8833 (mt) REVERT: A 4346 MET cc_start: 0.8982 (mmp) cc_final: 0.8753 (mmm) REVERT: A 4462 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7370 (tpp80) REVERT: A 4604 VAL cc_start: 0.8585 (t) cc_final: 0.8234 (p) outliers start: 78 outliers final: 51 residues processed: 340 average time/residue: 0.1487 time to fit residues: 80.0823 Evaluate side-chains 322 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1938 PHE Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2261 LYS Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3208 ILE Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4284 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4606 THR Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 247 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2485 GLN A2707 GLN A2827 HIS ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078576 restraints weight = 65593.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081110 restraints weight = 35180.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082767 restraints weight = 24037.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083822 restraints weight = 19049.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084491 restraints weight = 16535.892| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22340 Z= 0.143 Angle : 0.604 14.435 30308 Z= 0.292 Chirality : 0.040 0.284 3412 Planarity : 0.004 0.057 3883 Dihedral : 6.164 159.158 3012 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.12 % Allowed : 20.61 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.16), residues: 2699 helix: 1.93 (0.13), residues: 1524 sheet: -0.97 (0.33), residues: 220 loop : 0.22 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2358 TYR 0.022 0.001 TYR A2496 PHE 0.017 0.002 PHE A3496 TRP 0.015 0.001 TRP A2584 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00324 (22340) covalent geometry : angle 0.60416 (30308) hydrogen bonds : bond 0.03729 ( 1258) hydrogen bonds : angle 4.31817 ( 3675) *********************** 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 352 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.9291 (mmt) cc_final: 0.9014 (mmm) REVERT: A 1937 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7568 (p0) REVERT: A 1948 LEU cc_start: 0.9272 (mt) cc_final: 0.8864 (mt) REVERT: A 1958 ASP cc_start: 0.8533 (t0) cc_final: 0.7787 (m-30) REVERT: A 1959 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6626 (tp30) REVERT: A 1960 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 2099 SER cc_start: 0.9503 (m) cc_final: 0.9027 (p) REVERT: A 2149 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8797 (tp) REVERT: A 2302 VAL cc_start: 0.9074 (t) cc_final: 0.8781 (m) REVERT: A 2499 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8791 (mm) REVERT: A 2510 MET cc_start: 0.8320 (mpp) cc_final: 0.7750 (mtt) REVERT: A 2717 ASP cc_start: 0.7449 (t70) cc_final: 0.6888 (p0) REVERT: A 2720 ARG cc_start: 0.5649 (mmt-90) cc_final: 0.4615 (mpt180) REVERT: A 2847 ASP cc_start: 0.8971 (m-30) cc_final: 0.8659 (m-30) REVERT: A 2962 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7762 (pptt) REVERT: A 2994 MET cc_start: 0.8153 (mmm) cc_final: 0.7821 (tpp) REVERT: A 2996 GLU cc_start: 0.8150 (pm20) cc_final: 0.7841 (pm20) REVERT: A 3030 MET cc_start: 0.7950 (mmm) cc_final: 0.7504 (mmm) REVERT: A 3199 MET cc_start: 0.7055 (mtp) cc_final: 0.6840 (tmm) REVERT: A 3586 TYR cc_start: 0.8435 (m-80) cc_final: 0.8205 (m-10) REVERT: A 3591 ASP cc_start: 0.7671 (t0) cc_final: 0.6708 (p0) REVERT: A 3819 LYS cc_start: 0.9291 (ttpp) cc_final: 0.9081 (ttpp) REVERT: A 3873 ARG cc_start: 0.8491 (mmt180) cc_final: 0.8062 (mmm160) REVERT: A 3933 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8573 (mt-10) REVERT: A 3960 TRP cc_start: 0.8554 (t60) cc_final: 0.7916 (t60) REVERT: A 3991 LEU cc_start: 0.9249 (mt) cc_final: 0.8869 (mt) REVERT: A 4346 MET cc_start: 0.8942 (mmp) cc_final: 0.8717 (mmm) outliers start: 75 outliers final: 59 residues processed: 326 average time/residue: 0.1526 time to fit residues: 79.4673 Evaluate side-chains 327 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2048 LEU Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2261 LYS Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3109 PHE 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 3189 GLU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4284 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4606 THR Chi-restraints excluded: chain A residue 4618 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 244 optimal weight: 0.0010 chunk 79 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 82 optimal weight: 0.0020 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077242 restraints weight = 65738.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079703 restraints weight = 35576.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081314 restraints weight = 24499.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082378 restraints weight = 19478.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082936 restraints weight = 16863.477| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22340 Z= 0.170 Angle : 0.636 17.192 30308 Z= 0.309 Chirality : 0.041 0.273 3412 Planarity : 0.004 0.058 3883 Dihedral : 6.202 159.718 3012 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.32 % Allowed : 20.69 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.16), residues: 2699 helix: 1.85 (0.13), residues: 1520 sheet: -0.91 (0.32), residues: 234 loop : 0.18 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3611 TYR 0.022 0.001 TYR A2496 PHE 0.020 0.002 PHE A3496 TRP 0.032 0.002 TRP A2584 HIS 0.005 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00384 (22340) covalent geometry : angle 0.63613 (30308) hydrogen bonds : bond 0.03834 ( 1258) hydrogen bonds : angle 4.36807 ( 3675) *********************** 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 351 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 271 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6032 (mmm) cc_final: 0.5808 (mmp) REVERT: A 1892 MET cc_start: 0.9306 (mmt) cc_final: 0.9034 (mmm) REVERT: A 1937 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.7518 (p0) REVERT: A 1958 ASP cc_start: 0.8577 (t0) cc_final: 0.7835 (m-30) REVERT: A 1959 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6740 (tp30) REVERT: A 1960 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 2018 MET cc_start: 0.7606 (mtt) cc_final: 0.7403 (mtm) REVERT: A 2099 SER cc_start: 0.9509 (m) cc_final: 0.9053 (p) REVERT: A 2149 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8819 (tp) REVERT: A 2302 VAL cc_start: 0.9204 (t) cc_final: 0.8915 (m) REVERT: A 2332 ARG cc_start: 0.5261 (ppt170) cc_final: 0.5054 (ppt170) REVERT: A 2346 GLN cc_start: 0.7629 (pt0) cc_final: 0.7389 (pt0) REVERT: A 2510 MET cc_start: 0.8366 (mpp) cc_final: 0.7702 (mtt) REVERT: A 2584 TRP cc_start: 0.8314 (m-90) cc_final: 0.7553 (m-90) REVERT: A 2717 ASP cc_start: 0.7416 (t70) cc_final: 0.6914 (p0) REVERT: A 2847 ASP cc_start: 0.8939 (m-30) cc_final: 0.8626 (m-30) REVERT: A 2962 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7710 (pptt) REVERT: A 2994 MET cc_start: 0.8164 (mmm) cc_final: 0.7857 (tpp) REVERT: A 2996 GLU cc_start: 0.8138 (pm20) cc_final: 0.7804 (pm20) REVERT: A 3030 MET cc_start: 0.7817 (mmm) cc_final: 0.7408 (mmp) REVERT: A 3039 LYS cc_start: 0.9361 (mmtm) cc_final: 0.8958 (ttmt) REVERT: A 3500 MET cc_start: 0.7737 (mmm) cc_final: 0.7424 (mmm) REVERT: A 3567 LEU cc_start: 0.9153 (tp) cc_final: 0.8879 (mp) REVERT: A 3586 TYR cc_start: 0.8352 (m-80) cc_final: 0.8003 (m-10) REVERT: A 3591 ASP cc_start: 0.7674 (t0) cc_final: 0.6758 (p0) REVERT: A 3873 ARG cc_start: 0.8309 (mmt180) cc_final: 0.8079 (mmm160) REVERT: A 3933 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8491 (mt-10) REVERT: A 3960 TRP cc_start: 0.8517 (t60) cc_final: 0.7737 (t60) REVERT: A 3991 LEU cc_start: 0.9265 (mt) cc_final: 0.8895 (mt) REVERT: A 4346 MET cc_start: 0.8930 (mmp) cc_final: 0.8727 (mmm) outliers start: 80 outliers final: 62 residues processed: 322 average time/residue: 0.1494 time to fit residues: 77.1631 Evaluate side-chains 316 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 251 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2731 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3109 PHE 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 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4284 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4606 THR Chi-restraints excluded: chain A residue 4618 LEU Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 260 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2271 ASN ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078139 restraints weight = 65525.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080648 restraints weight = 35178.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082281 restraints weight = 24101.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083345 restraints weight = 19161.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083903 restraints weight = 16637.498| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22340 Z= 0.130 Angle : 0.625 15.268 30308 Z= 0.301 Chirality : 0.041 0.257 3412 Planarity : 0.004 0.055 3883 Dihedral : 6.145 161.233 3012 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.87 % Allowed : 21.27 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.16), residues: 2699 helix: 1.91 (0.13), residues: 1524 sheet: -0.95 (0.33), residues: 222 loop : 0.20 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3611 TYR 0.025 0.001 TYR A2496 PHE 0.033 0.002 PHE A2635 TRP 0.023 0.001 TRP A2584 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00289 (22340) covalent geometry : angle 0.62492 (30308) hydrogen bonds : bond 0.03722 ( 1258) hydrogen bonds : angle 4.29420 ( 3675) *********************** 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 335 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5865 (mmm) cc_final: 0.5198 (mmm) REVERT: A 1892 MET cc_start: 0.9299 (mmt) cc_final: 0.9018 (mmm) REVERT: A 1937 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7531 (p0) REVERT: A 1958 ASP cc_start: 0.8555 (t0) cc_final: 0.7866 (m-30) REVERT: A 1960 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 2099 SER cc_start: 0.9491 (m) cc_final: 0.9015 (p) REVERT: A 2149 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 2189 MET cc_start: 0.8700 (ttm) cc_final: 0.7882 (ttm) REVERT: A 2302 VAL cc_start: 0.9185 (t) cc_final: 0.8897 (m) REVERT: A 2313 GLU cc_start: 0.8069 (pp20) cc_final: 0.7608 (mp0) REVERT: A 2332 ARG cc_start: 0.5288 (ppt170) cc_final: 0.5057 (ppt170) REVERT: A 2346 GLN cc_start: 0.7593 (pt0) cc_final: 0.7345 (pt0) REVERT: A 2510 MET cc_start: 0.8368 (mpp) cc_final: 0.7683 (mtt) REVERT: A 2671 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.4959 (ppp) REVERT: A 2717 ASP cc_start: 0.7475 (t70) cc_final: 0.6970 (p0) REVERT: A 2775 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: A 2847 ASP cc_start: 0.8923 (m-30) cc_final: 0.8624 (m-30) REVERT: A 2914 GLU cc_start: 0.8495 (mp0) cc_final: 0.8165 (mp0) REVERT: A 2962 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7705 (pptt) REVERT: A 2994 MET cc_start: 0.8112 (mmm) cc_final: 0.7840 (tpp) REVERT: A 2996 GLU cc_start: 0.8185 (pm20) cc_final: 0.7843 (pm20) REVERT: A 3030 MET cc_start: 0.7875 (mmm) cc_final: 0.7438 (mmp) REVERT: A 3039 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8909 (ttmt) REVERT: A 3169 MET cc_start: 0.7674 (tpp) cc_final: 0.7404 (mmm) REVERT: A 3500 MET cc_start: 0.7911 (mmm) cc_final: 0.7652 (mmm) REVERT: A 3586 TYR cc_start: 0.8382 (m-80) cc_final: 0.8177 (m-10) REVERT: A 3591 ASP cc_start: 0.7694 (t0) cc_final: 0.6723 (p0) REVERT: A 3873 ARG cc_start: 0.8344 (mmt180) cc_final: 0.8108 (mmm160) REVERT: A 3933 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8532 (mt-10) REVERT: A 3960 TRP cc_start: 0.8530 (t60) cc_final: 0.7763 (t60) REVERT: A 3991 LEU cc_start: 0.9259 (mt) cc_final: 0.8881 (mt) REVERT: A 4328 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 4346 MET cc_start: 0.8893 (mmp) cc_final: 0.8684 (mmm) outliers start: 69 outliers final: 56 residues processed: 311 average time/residue: 0.1485 time to fit residues: 74.1742 Evaluate side-chains 317 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2731 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3109 PHE 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 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4284 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4606 THR Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 217 optimal weight: 4.9990 chunk 266 optimal weight: 0.0670 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 overall best weight: 1.2722 ------------------------------------------------------------------------------- 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** A1863 ASN A1939 GLN ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078044 restraints weight = 65252.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080490 restraints weight = 35124.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082137 restraints weight = 24177.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083217 restraints weight = 19165.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083852 restraints weight = 16596.047| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22340 Z= 0.135 Angle : 0.630 15.235 30308 Z= 0.303 Chirality : 0.041 0.246 3412 Planarity : 0.004 0.054 3883 Dihedral : 6.115 163.279 3012 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 21.52 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.17), residues: 2699 helix: 1.94 (0.13), residues: 1517 sheet: -0.88 (0.32), residues: 229 loop : 0.17 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3611 TYR 0.027 0.001 TYR A2496 PHE 0.018 0.001 PHE A3496 TRP 0.032 0.001 TRP A2584 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00306 (22340) covalent geometry : angle 0.63009 (30308) hydrogen bonds : bond 0.03695 ( 1258) hydrogen bonds : angle 4.26939 ( 3675) ********************** 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 325 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5772 (mmm) cc_final: 0.5163 (mmm) REVERT: A 1892 MET cc_start: 0.9300 (mmt) cc_final: 0.8973 (mmm) REVERT: A 1937 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7381 (p0) REVERT: A 1958 ASP cc_start: 0.8543 (t0) cc_final: 0.7836 (m-30) REVERT: A 1960 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7632 (t80) REVERT: A 1967 MET cc_start: 0.8824 (mmm) cc_final: 0.8552 (mmm) REVERT: A 2099 SER cc_start: 0.9486 (m) cc_final: 0.8981 (p) REVERT: A 2149 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8823 (tp) REVERT: A 2302 VAL cc_start: 0.9201 (t) cc_final: 0.8915 (m) REVERT: A 2313 GLU cc_start: 0.8310 (pp20) cc_final: 0.7501 (mp0) REVERT: A 2346 GLN cc_start: 0.7502 (pt0) cc_final: 0.7180 (pt0) REVERT: A 2510 MET cc_start: 0.8313 (mpp) cc_final: 0.7656 (mtt) REVERT: A 2584 TRP cc_start: 0.8301 (m-90) cc_final: 0.7495 (m-90) REVERT: A 2671 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.4990 (ppp) REVERT: A 2717 ASP cc_start: 0.7464 (t70) cc_final: 0.6886 (p0) REVERT: A 2720 ARG cc_start: 0.5727 (mmt-90) cc_final: 0.4759 (mpt180) REVERT: A 2775 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: A 2847 ASP cc_start: 0.8927 (m-30) cc_final: 0.8636 (m-30) REVERT: A 2914 GLU cc_start: 0.8373 (mp0) cc_final: 0.8074 (mp0) REVERT: A 2962 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7708 (pptt) REVERT: A 2994 MET cc_start: 0.8092 (mmm) cc_final: 0.7853 (tpp) REVERT: A 2996 GLU cc_start: 0.8206 (pm20) cc_final: 0.7864 (pm20) REVERT: A 3030 MET cc_start: 0.7739 (mmm) cc_final: 0.7371 (mmp) REVERT: A 3039 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8904 (ttmt) REVERT: A 3169 MET cc_start: 0.7680 (tpp) cc_final: 0.7434 (mmm) REVERT: A 3586 TYR cc_start: 0.8406 (m-80) cc_final: 0.8093 (m-10) REVERT: A 3591 ASP cc_start: 0.7639 (t0) cc_final: 0.6690 (p0) REVERT: A 3933 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 3960 TRP cc_start: 0.8536 (t60) cc_final: 0.7735 (t60) REVERT: A 4296 MET cc_start: 0.9089 (tmm) cc_final: 0.8175 (tmm) REVERT: A 4328 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 4346 MET cc_start: 0.8869 (mmp) cc_final: 0.8645 (mmm) outliers start: 67 outliers final: 57 residues processed: 300 average time/residue: 0.1534 time to fit residues: 73.1028 Evaluate side-chains 315 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2678 ARG Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2731 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2850 ILE Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 3109 PHE 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 3155 HIS Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3496 PHE Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4284 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4553 LEU Chi-restraints excluded: chain A residue 4606 THR Chi-restraints excluded: chain A residue 4628 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 212 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078774 restraints weight = 64966.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081289 restraints weight = 35010.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082940 restraints weight = 24011.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084013 restraints weight = 19062.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084650 restraints weight = 16540.631| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22340 Z= 0.120 Angle : 0.631 14.566 30308 Z= 0.301 Chirality : 0.041 0.237 3412 Planarity : 0.004 0.073 3883 Dihedral : 6.061 165.323 3012 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.58 % Allowed : 21.85 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.17), residues: 2699 helix: 2.00 (0.13), residues: 1517 sheet: -0.79 (0.33), residues: 225 loop : 0.18 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3611 TYR 0.026 0.001 TYR A2496 PHE 0.022 0.001 PHE A3496 TRP 0.027 0.001 TRP A2584 HIS 0.006 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00269 (22340) covalent geometry : angle 0.63142 (30308) hydrogen bonds : bond 0.03606 ( 1258) hydrogen bonds : angle 4.21481 ( 3675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.03 seconds wall clock time: 73 minutes 16.02 seconds (4396.02 seconds total)