Starting phenix.real_space_refine on Thu May 22 02:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmn_44704/05_2025/9bmn_44704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmn_44704/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmn_44704/05_2025/9bmn_44704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmn_44704/05_2025/9bmn_44704.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmn_44704/05_2025/9bmn_44704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmn_44704/05_2025/9bmn_44704.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.26, per 1000 atoms: 0.56 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: 5.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 18 sheets defined 61.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 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: 12.40 Time building geometry restraints manager: 6.50 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 54.080 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.620 ------------------------------------------------------------------------------- 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 : 12.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (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 TRP 0.023 0.001 TRP A2825 HIS 0.005 0.001 HIS A2689 PHE 0.028 0.002 PHE A3513 TYR 0.017 0.001 TYR A3812 ARG 0.006 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.13539 ( 1258) hydrogen bonds : angle 5.75988 ( 3675) covalent geometry : bond 0.00356 (22340) covalent geometry : angle 0.64721 (30308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 669 time to evaluate : 2.437 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: 0.8576 (t) REVERT: A 1879 LEU cc_start: 0.7248 (tp) cc_final: 0.5781 (tp) REVERT: A 1892 MET cc_start: 0.8691 (mmt) cc_final: 0.8358 (mmm) REVERT: A 1959 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7306 (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: 0.8587 (p) REVERT: A 2097 LEU cc_start: 0.9304 (mm) cc_final: 0.9031 (mt) REVERT: A 2099 SER cc_start: 0.9153 (m) cc_final: 0.8681 (p) REVERT: A 2279 LEU cc_start: 0.8358 (tp) cc_final: 0.7629 (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: 0.8814 (p) REVERT: A 4124 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7334 (tp) REVERT: A 4247 MET cc_start: 0.8453 (mtm) cc_final: 0.8203 (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: 0.7789 (pt) outliers start: 6 outliers final: 0 residues processed: 672 average time/residue: 0.3834 time to fit residues: 383.6476 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 : 2.321 ------------------------------------------------------------------------------- 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 228 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080071 restraints weight = 64783.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082548 restraints weight = 35465.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084199 restraints weight = 24515.021| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22340 Z= 0.226 Angle : 0.704 9.671 30308 Z= 0.353 Chirality : 0.042 0.192 3412 Planarity : 0.005 0.069 3883 Dihedral : 7.223 152.443 3014 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.20 % Allowed : 18.61 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2699 helix: 1.62 (0.13), residues: 1536 sheet: -1.13 (0.33), residues: 223 loop : 0.20 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2825 HIS 0.010 0.001 HIS A2725 PHE 0.024 0.002 PHE A4613 TYR 0.025 0.002 TYR A3519 ARG 0.008 0.001 ARG A4415 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1258) hydrogen bonds : angle 4.87595 ( 3675) covalent geometry : bond 0.00510 (22340) covalent geometry : angle 0.70393 (30308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.9156 (mmt) cc_final: 0.8843 (mmm) REVERT: A 1958 ASP cc_start: 0.8386 (t0) cc_final: 0.8145 (t0) REVERT: A 1959 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 2012 MET cc_start: 0.9009 (tpp) cc_final: 0.8616 (tpp) REVERT: A 2084 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 2099 SER cc_start: 0.9486 (m) cc_final: 0.9043 (p) REVERT: A 2157 LEU cc_start: 0.9130 (tp) cc_final: 0.8924 (tt) REVERT: A 2273 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5639 (ttp80) REVERT: A 2284 LEU cc_start: 0.8702 (mt) cc_final: 0.8493 (mt) REVERT: A 2510 MET cc_start: 0.8191 (mpp) cc_final: 0.7766 (ptp) REVERT: A 2717 ASP cc_start: 0.7268 (t70) cc_final: 0.6974 (p0) REVERT: A 2847 ASP cc_start: 0.9020 (m-30) cc_final: 0.8713 (m-30) REVERT: A 2962 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7653 (pptt) REVERT: A 2994 MET cc_start: 0.8060 (mmm) cc_final: 0.7150 (tpp) REVERT: A 3030 MET cc_start: 0.7365 (mmm) cc_final: 0.6932 (mmm) REVERT: A 3078 ARG cc_start: 0.8821 (mmp80) cc_final: 0.8040 (mmp80) REVERT: A 3199 MET cc_start: 0.7081 (mtp) cc_final: 0.6797 (tmm) REVERT: A 3586 TYR cc_start: 0.8279 (m-80) cc_final: 0.7804 (m-10) REVERT: A 3591 ASP cc_start: 0.7264 (t0) cc_final: 0.6407 (p0) REVERT: A 3683 ASP cc_start: 0.8959 (t0) cc_final: 0.8488 (t0) REVERT: A 3801 TYR cc_start: 0.8369 (m-10) cc_final: 0.8163 (m-10) REVERT: A 3873 ARG cc_start: 0.8306 (mmt180) cc_final: 0.8004 (mmm160) REVERT: A 3960 TRP cc_start: 0.8469 (t60) cc_final: 0.7565 (t60) REVERT: A 4195 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8138 (mtm110) REVERT: A 4377 MET cc_start: 0.6426 (tmm) cc_final: 0.5827 (ppp) REVERT: A 4604 VAL cc_start: 0.8625 (t) cc_final: 0.8211 (p) outliers start: 77 outliers final: 41 residues processed: 384 average time/residue: 0.3523 time to fit residues: 208.0653 Evaluate side-chains 309 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL 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 2281 THR 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 2374 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2747 ILE 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 3609 ILE 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 3818 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 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 139 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 252 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** A1979 GLN A2482 GLN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3032 GLN A3538 GLN A3906 GLN A4491 ASN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.107523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081374 restraints weight = 63796.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083896 restraints weight = 34938.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085543 restraints weight = 24018.295| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22340 Z= 0.137 Angle : 0.622 10.690 30308 Z= 0.303 Chirality : 0.041 0.347 3412 Planarity : 0.004 0.059 3883 Dihedral : 6.850 150.586 3012 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.78 % Allowed : 19.61 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2699 helix: 1.75 (0.13), residues: 1537 sheet: -1.16 (0.32), residues: 226 loop : 0.22 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2825 HIS 0.006 0.001 HIS A2791 PHE 0.020 0.002 PHE A4613 TYR 0.019 0.001 TYR A3641 ARG 0.006 0.000 ARG A4329 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 1258) hydrogen bonds : angle 4.55737 ( 3675) covalent geometry : bond 0.00299 (22340) covalent geometry : angle 0.62182 (30308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 2.356 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: 0.9157 (mmt) cc_final: 0.8814 (mmm) REVERT: A 1937 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.7572 (p0) REVERT: A 1958 ASP cc_start: 0.8405 (t0) cc_final: 0.7784 (m-30) REVERT: A 1959 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6192 (tp30) REVERT: A 1979 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: A 2012 MET cc_start: 0.8898 (tpp) cc_final: 0.8586 (tpp) REVERT: A 2084 SER cc_start: 0.9014 (m) cc_final: 0.8492 (p) REVERT: A 2099 SER cc_start: 0.9442 (m) cc_final: 0.8997 (p) REVERT: A 2273 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6512 (ttp80) REVERT: A 2361 MET cc_start: 0.7642 (tpp) cc_final: 0.7214 (tpp) REVERT: A 2461 MET cc_start: 0.8576 (ttp) cc_final: 0.7809 (ptm) REVERT: A 2493 TYR cc_start: 0.8488 (t80) cc_final: 0.7522 (t80) REVERT: A 2510 MET cc_start: 0.8184 (mpp) cc_final: 0.7814 (ptp) REVERT: A 2717 ASP cc_start: 0.7251 (t70) cc_final: 0.6950 (p0) REVERT: A 2847 ASP cc_start: 0.8976 (m-30) cc_final: 0.8679 (m-30) REVERT: A 2933 LEU cc_start: 0.9102 (mt) cc_final: 0.8894 (mp) REVERT: A 2962 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7630 (pptt) REVERT: A 2967 TYR cc_start: 0.7221 (t80) cc_final: 0.6988 (t80) REVERT: A 2994 MET cc_start: 0.8231 (mmm) cc_final: 0.7430 (tpp) REVERT: A 3030 MET cc_start: 0.7340 (mmm) cc_final: 0.6917 (mmm) REVERT: A 3078 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8242 (mmp80) REVERT: A 3199 MET cc_start: 0.7151 (mtp) cc_final: 0.6898 (tmm) REVERT: A 3500 MET cc_start: 0.7648 (mmm) cc_final: 0.7388 (mmm) REVERT: A 3547 ILE cc_start: 0.6871 (tp) cc_final: 0.6558 (tp) REVERT: A 3586 TYR cc_start: 0.8289 (m-80) cc_final: 0.7594 (m-10) REVERT: A 3591 ASP cc_start: 0.7538 (t0) cc_final: 0.6561 (p0) REVERT: A 3683 ASP cc_start: 0.8809 (t0) cc_final: 0.8476 (t0) REVERT: A 3801 TYR cc_start: 0.8384 (m-10) cc_final: 0.8121 (m-10) REVERT: A 3873 ARG cc_start: 0.8312 (mmt180) cc_final: 0.7928 (mmm160) REVERT: A 3960 TRP cc_start: 0.8482 (t60) cc_final: 0.7579 (t60) REVERT: A 4195 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8021 (mtm110) REVERT: A 4296 MET cc_start: 0.8859 (tmm) cc_final: 0.8206 (tmm) REVERT: A 4422 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8364 (tmmt) REVERT: A 4604 VAL cc_start: 0.8430 (t) cc_final: 0.8023 (p) outliers start: 67 outliers final: 31 residues processed: 362 average time/residue: 0.3401 time to fit residues: 191.1539 Evaluate side-chains 311 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 1929 VAL Chi-restraints excluded: chain A residue 1937 ASP 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 2149 LEU 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 2466 CYS Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2747 ILE 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 3189 GLU 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 3933 GLU 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 4553 LEU Chi-restraints excluded: chain A residue 4614 THR 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 53 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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** ** A2442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2789 GLN ** A3799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082108 restraints weight = 65037.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084688 restraints weight = 35449.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086378 restraints weight = 24390.604| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22340 Z= 0.168 Angle : 0.617 9.006 30308 Z= 0.303 Chirality : 0.041 0.277 3412 Planarity : 0.004 0.050 3883 Dihedral : 6.611 152.417 3012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.16 % Allowed : 19.28 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2699 helix: 1.79 (0.13), residues: 1540 sheet: -1.06 (0.33), residues: 217 loop : 0.24 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2825 HIS 0.005 0.001 HIS A2791 PHE 0.029 0.002 PHE A4613 TYR 0.021 0.001 TYR A2496 ARG 0.006 0.000 ARG A2358 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 1258) hydrogen bonds : angle 4.52468 ( 3675) covalent geometry : bond 0.00378 (22340) covalent geometry : angle 0.61682 (30308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 2.522 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: A 1892 MET cc_start: 0.9064 (mmt) cc_final: 0.8794 (mmm) REVERT: A 1937 ASP cc_start: 0.8539 (p0) cc_final: 0.7517 (p0) REVERT: A 1958 ASP cc_start: 0.8415 (t0) cc_final: 0.7857 (m-30) REVERT: A 1959 GLU cc_start: 0.7764 (mm-30) cc_final: 0.6484 (tp30) REVERT: A 1960 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 2012 MET cc_start: 0.8862 (tpp) cc_final: 0.8646 (tpp) REVERT: A 2084 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 2099 SER cc_start: 0.9429 (m) cc_final: 0.8999 (p) REVERT: A 2130 ASN cc_start: 0.8877 (m110) cc_final: 0.8578 (p0) REVERT: A 2149 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 2273 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6495 (ttp80) REVERT: A 2510 MET cc_start: 0.8131 (mpp) cc_final: 0.7462 (mtt) REVERT: A 2717 ASP cc_start: 0.7197 (t70) cc_final: 0.6966 (p0) REVERT: A 2847 ASP cc_start: 0.8932 (m-30) cc_final: 0.8651 (m-30) REVERT: A 2962 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7657 (pptt) REVERT: A 3030 MET cc_start: 0.7937 (mmm) cc_final: 0.7437 (mmm) REVERT: A 3078 ARG cc_start: 0.8648 (mmp80) cc_final: 0.8210 (mmp80) REVERT: A 3199 MET cc_start: 0.7159 (mtp) cc_final: 0.6930 (tmm) REVERT: A 3547 ILE cc_start: 0.6939 (tp) cc_final: 0.6630 (tp) REVERT: A 3586 TYR cc_start: 0.8373 (m-80) cc_final: 0.8090 (m-10) REVERT: A 3591 ASP cc_start: 0.7568 (t0) cc_final: 0.6505 (p0) REVERT: A 3873 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7931 (mmm160) REVERT: A 4099 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8738 (p) REVERT: A 4195 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8082 (mtm110) REVERT: A 4296 MET cc_start: 0.8956 (tmm) cc_final: 0.8235 (tmm) REVERT: A 4604 VAL cc_start: 0.8577 (t) cc_final: 0.8189 (p) outliers start: 76 outliers final: 47 residues processed: 325 average time/residue: 0.3401 time to fit residues: 175.1118 Evaluate side-chains 311 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 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 2345 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2747 ILE 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 2976 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 3496 PHE 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 3731 LEU Chi-restraints excluded: chain A residue 3821 ILE Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3933 GLU 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 4481 ASP 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 97 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 229 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 A2439 HIS A2752 ASN A4012 ASN A4187 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.111617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085644 restraints weight = 66158.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088355 restraints weight = 35304.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090076 restraints weight = 24171.734| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.127 Angle : 0.595 10.179 30308 Z= 0.288 Chirality : 0.040 0.332 3412 Planarity : 0.004 0.049 3883 Dihedral : 6.320 153.102 3012 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.03 % Allowed : 20.36 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.16), residues: 2699 helix: 1.89 (0.13), residues: 1539 sheet: -1.00 (0.33), residues: 217 loop : 0.25 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2825 HIS 0.006 0.001 HIS A2791 PHE 0.030 0.002 PHE A2635 TYR 0.021 0.001 TYR A2496 ARG 0.004 0.000 ARG A2358 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1258) hydrogen bonds : angle 4.40187 ( 3675) covalent geometry : bond 0.00281 (22340) covalent geometry : angle 0.59462 (30308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 295 time to evaluate : 2.490 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: 0.5771 (mmm) cc_final: 0.4972 (mmm) REVERT: A 1892 MET cc_start: 0.9064 (mmt) cc_final: 0.8794 (mmm) REVERT: A 1937 ASP cc_start: 0.8480 (p0) cc_final: 0.7470 (p0) REVERT: A 1958 ASP cc_start: 0.8375 (t0) cc_final: 0.7782 (m-30) REVERT: A 1959 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6748 (tp30) REVERT: A 1960 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 1979 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: A 2012 MET cc_start: 0.8799 (tpp) cc_final: 0.8587 (tpp) REVERT: A 2084 SER cc_start: 0.9028 (m) cc_final: 0.8517 (p) REVERT: A 2099 SER cc_start: 0.9440 (m) cc_final: 0.8982 (p) REVERT: A 2130 ASN cc_start: 0.8835 (m110) cc_final: 0.8579 (p0) REVERT: A 2149 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 2273 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6679 (ttp80) REVERT: A 2493 TYR cc_start: 0.8558 (t80) cc_final: 0.7749 (t80) REVERT: A 2510 MET cc_start: 0.8150 (mpp) cc_final: 0.7548 (mtt) REVERT: A 2635 PHE cc_start: 0.8589 (m-80) cc_final: 0.8345 (m-80) REVERT: A 2717 ASP cc_start: 0.7201 (t70) cc_final: 0.6951 (p0) REVERT: A 2847 ASP cc_start: 0.8887 (m-30) cc_final: 0.8605 (m-30) REVERT: A 2962 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7552 (pptt) REVERT: A 2994 MET cc_start: 0.8253 (mmm) cc_final: 0.7611 (tpp) REVERT: A 3030 MET cc_start: 0.7909 (mmm) cc_final: 0.7405 (mmm) REVERT: A 3199 MET cc_start: 0.7109 (mtp) cc_final: 0.6905 (tmm) REVERT: A 3547 ILE cc_start: 0.6889 (tp) cc_final: 0.6647 (tp) REVERT: A 3586 TYR cc_start: 0.8372 (m-80) cc_final: 0.8166 (m-10) REVERT: A 3591 ASP cc_start: 0.7574 (t0) cc_final: 0.6473 (p0) REVERT: A 3819 LYS cc_start: 0.9273 (ttpp) cc_final: 0.9040 (ttpp) REVERT: A 3873 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7865 (mmm160) REVERT: A 3929 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.7770 (m) REVERT: A 3960 TRP cc_start: 0.8381 (t60) cc_final: 0.7732 (t60) REVERT: A 3991 LEU cc_start: 0.9202 (mt) cc_final: 0.8853 (mt) REVERT: A 4195 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8105 (mtm110) REVERT: A 4296 MET cc_start: 0.8958 (tmm) cc_final: 0.8183 (tmm) REVERT: A 4462 ARG cc_start: 0.7352 (tpp80) cc_final: 0.7125 (tpp80) REVERT: A 4604 VAL cc_start: 0.8503 (t) cc_final: 0.8123 (p) outliers start: 73 outliers final: 46 residues processed: 348 average time/residue: 0.3368 time to fit residues: 185.3133 Evaluate side-chains 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 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 2149 LEU 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 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 2592 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2747 ILE 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 3133 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 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 3802 LEU Chi-restraints excluded: chain A residue 3929 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 4274 THR 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 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 6 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3875 r_free = 0.3875 target = 0.111729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088172 restraints weight = 65846.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090006 restraints weight = 36734.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091171 restraints weight = 24589.054| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22340 Z= 0.122 Angle : 0.599 10.440 30308 Z= 0.289 Chirality : 0.040 0.299 3412 Planarity : 0.004 0.049 3883 Dihedral : 6.229 155.204 3012 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 20.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2699 helix: 1.93 (0.13), residues: 1535 sheet: -0.93 (0.33), residues: 217 loop : 0.27 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2584 HIS 0.006 0.001 HIS A2791 PHE 0.021 0.001 PHE A4613 TYR 0.021 0.001 TYR A2496 ARG 0.005 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1258) hydrogen bonds : angle 4.35706 ( 3675) covalent geometry : bond 0.00272 (22340) covalent geometry : angle 0.59892 (30308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 2.651 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: A 1892 MET cc_start: 0.9054 (mmt) cc_final: 0.8830 (mmm) REVERT: A 1937 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7471 (p0) REVERT: A 1958 ASP cc_start: 0.8311 (t0) cc_final: 0.7822 (m-30) REVERT: A 1960 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 2084 SER cc_start: 0.9103 (m) cc_final: 0.8680 (p) REVERT: A 2099 SER cc_start: 0.9404 (m) cc_final: 0.8924 (p) REVERT: A 2130 ASN cc_start: 0.8813 (m110) cc_final: 0.8547 (p0) REVERT: A 2273 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6716 (ttp80) REVERT: A 2493 TYR cc_start: 0.8598 (t80) cc_final: 0.7825 (t80) REVERT: A 2510 MET cc_start: 0.8183 (mpp) cc_final: 0.7581 (mtt) REVERT: A 2717 ASP cc_start: 0.7258 (t70) cc_final: 0.6974 (p0) REVERT: A 2847 ASP cc_start: 0.8857 (m-30) cc_final: 0.8597 (m-30) REVERT: A 2962 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7585 (pptt) REVERT: A 2994 MET cc_start: 0.8228 (mmm) cc_final: 0.7813 (tpp) REVERT: A 3030 MET cc_start: 0.8016 (mmm) cc_final: 0.7567 (mmm) REVERT: A 3068 MET cc_start: 0.8111 (mtp) cc_final: 0.7866 (mtp) REVERT: A 3078 ARG cc_start: 0.8804 (mmp80) cc_final: 0.8510 (mmm-85) REVERT: A 3199 MET cc_start: 0.7182 (mtp) cc_final: 0.6966 (tmm) REVERT: A 3547 ILE cc_start: 0.6873 (tp) cc_final: 0.6547 (tp) REVERT: A 3586 TYR cc_start: 0.8348 (m-80) cc_final: 0.8008 (m-10) REVERT: A 3591 ASP cc_start: 0.7562 (t0) cc_final: 0.6670 (p0) REVERT: A 3873 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7851 (mmm160) REVERT: A 3960 TRP cc_start: 0.8483 (t60) cc_final: 0.7835 (t60) REVERT: A 3991 LEU cc_start: 0.9195 (mt) cc_final: 0.8835 (mt) REVERT: A 4195 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8151 (mtm110) REVERT: A 4296 MET cc_start: 0.8913 (tmm) cc_final: 0.8259 (tmm) REVERT: A 4462 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7148 (tpp80) REVERT: A 4604 VAL cc_start: 0.8420 (t) cc_final: 0.8011 (p) outliers start: 72 outliers final: 51 residues processed: 331 average time/residue: 0.3303 time to fit residues: 173.4039 Evaluate side-chains 321 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2149 LEU Chi-restraints excluded: chain A residue 2261 LYS 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 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE 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 2731 VAL Chi-restraints excluded: chain A residue 2747 ILE 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 2946 LEU Chi-restraints excluded: chain A residue 2976 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 3189 GLU 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 3677 ILE 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 5 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A1979 GLN ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2707 GLN A3198 GLN ** A3799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3726 r_free = 0.3726 target = 0.106363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080195 restraints weight = 65202.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082777 restraints weight = 34858.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084472 restraints weight = 23693.677| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4421 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= 0.119 Angle : 0.597 13.796 30308 Z= 0.287 Chirality : 0.040 0.253 3412 Planarity : 0.004 0.045 3883 Dihedral : 6.154 157.547 3012 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.03 % Allowed : 20.48 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2699 helix: 1.98 (0.13), residues: 1530 sheet: -0.82 (0.32), residues: 228 loop : 0.24 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2234 HIS 0.008 0.001 HIS A1779 PHE 0.020 0.001 PHE A4613 TYR 0.020 0.001 TYR A2496 ARG 0.005 0.000 ARG A3937 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1258) hydrogen bonds : angle 4.28847 ( 3675) covalent geometry : bond 0.00264 (22340) covalent geometry : angle 0.59693 (30308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 2.504 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: A 1657 MET cc_start: 0.5362 (mmm) cc_final: 0.4584 (mmm) REVERT: A 1892 MET cc_start: 0.9259 (mmt) cc_final: 0.9027 (mmm) REVERT: A 1937 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7555 (p0) REVERT: A 1958 ASP cc_start: 0.8440 (t0) cc_final: 0.7803 (m-30) REVERT: A 1960 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 1965 GLU cc_start: 0.8759 (mp0) cc_final: 0.7731 (mp0) REVERT: A 1979 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8261 (tp40) REVERT: A 2084 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 2099 SER cc_start: 0.9488 (m) cc_final: 0.8980 (p) REVERT: A 2130 ASN cc_start: 0.8860 (m110) cc_final: 0.8579 (p0) REVERT: A 2149 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8781 (tp) REVERT: A 2273 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6471 (ttp80) REVERT: A 2493 TYR cc_start: 0.8545 (t80) cc_final: 0.7697 (t80) REVERT: A 2510 MET cc_start: 0.8320 (mpp) cc_final: 0.7740 (mtt) REVERT: A 2704 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 2717 ASP cc_start: 0.7485 (t70) cc_final: 0.6952 (p0) REVERT: A 2799 MET cc_start: 0.7297 (ttm) cc_final: 0.6878 (ttm) REVERT: A 2847 ASP cc_start: 0.8944 (m-30) cc_final: 0.8652 (m-30) REVERT: A 2962 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7437 (pptt) REVERT: A 2994 MET cc_start: 0.8080 (mmm) cc_final: 0.7695 (tpp) REVERT: A 3030 MET cc_start: 0.8015 (mmm) cc_final: 0.7568 (mmp) REVERT: A 3039 LYS cc_start: 0.9366 (mmtm) cc_final: 0.8979 (ttmt) REVERT: A 3078 ARG cc_start: 0.8864 (mmp80) cc_final: 0.8523 (mmp80) REVERT: A 3199 MET cc_start: 0.7159 (mtp) cc_final: 0.6883 (tmm) REVERT: A 3567 LEU cc_start: 0.9161 (mt) cc_final: 0.8927 (mt) REVERT: A 3586 TYR cc_start: 0.8417 (m-80) cc_final: 0.8134 (m-10) REVERT: A 3591 ASP cc_start: 0.7678 (t0) cc_final: 0.6573 (p0) REVERT: A 3873 ARG cc_start: 0.8402 (mmt180) cc_final: 0.7971 (mmm160) REVERT: A 3960 TRP cc_start: 0.8571 (t60) cc_final: 0.7947 (t60) REVERT: A 3991 LEU cc_start: 0.9241 (mt) cc_final: 0.8852 (mt) REVERT: A 4063 ASN cc_start: 0.8691 (t0) cc_final: 0.8461 (t0) REVERT: A 4195 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8261 (mtm110) REVERT: A 4296 MET cc_start: 0.8960 (tmm) cc_final: 0.8225 (tmm) REVERT: A 4462 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7205 (tpp80) REVERT: A 4544 ASN cc_start: 0.8268 (t0) cc_final: 0.7975 (t0) REVERT: A 4604 VAL cc_start: 0.8496 (t) cc_final: 0.8104 (p) outliers start: 73 outliers final: 50 residues processed: 339 average time/residue: 0.3337 time to fit residues: 179.9431 Evaluate side-chains 326 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1979 GLN Chi-restraints excluded: chain A residue 2084 SER 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 2272 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 2339 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE 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 2846 THR Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2976 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 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 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 4107 MET Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4256 VAL Chi-restraints excluded: chain A residue 4274 THR 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 131 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** A1939 GLN A1979 GLN A2707 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.106131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080214 restraints weight = 64999.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082804 restraints weight = 34604.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084515 restraints weight = 23473.064| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4578 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= 0.122 Angle : 0.605 12.768 30308 Z= 0.292 Chirality : 0.040 0.254 3412 Planarity : 0.004 0.045 3883 Dihedral : 6.070 158.280 3012 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 21.23 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.16), residues: 2699 helix: 1.99 (0.13), residues: 1524 sheet: -0.81 (0.33), residues: 225 loop : 0.27 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2584 HIS 0.008 0.001 HIS A1779 PHE 0.023 0.001 PHE A1870 TYR 0.020 0.001 TYR A2496 ARG 0.005 0.000 ARG A2358 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1258) hydrogen bonds : angle 4.26729 ( 3675) covalent geometry : bond 0.00272 (22340) covalent geometry : angle 0.60516 (30308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 2.409 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: A 1892 MET cc_start: 0.9278 (mmt) cc_final: 0.9029 (mmm) REVERT: A 1937 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.7564 (p0) REVERT: A 1948 LEU cc_start: 0.9239 (mt) cc_final: 0.8841 (mt) REVERT: A 1958 ASP cc_start: 0.8469 (t0) cc_final: 0.7844 (m-30) REVERT: A 1965 GLU cc_start: 0.8754 (mp0) cc_final: 0.8513 (mp0) REVERT: A 2084 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8645 (p) REVERT: A 2099 SER cc_start: 0.9487 (m) cc_final: 0.8967 (p) REVERT: A 2130 ASN cc_start: 0.8852 (m110) cc_final: 0.8585 (p0) REVERT: A 2149 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 2220 LEU cc_start: 0.8803 (tp) cc_final: 0.8530 (tt) REVERT: A 2273 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6559 (ttp80) REVERT: A 2493 TYR cc_start: 0.8559 (t80) cc_final: 0.7786 (t80) REVERT: A 2510 MET cc_start: 0.8400 (mpp) cc_final: 0.7909 (mtt) REVERT: A 2717 ASP cc_start: 0.7551 (t70) cc_final: 0.6946 (p0) REVERT: A 2720 ARG cc_start: 0.5597 (mmt-90) cc_final: 0.4730 (mpt180) REVERT: A 2799 MET cc_start: 0.7331 (ttm) cc_final: 0.6626 (ttm) REVERT: A 2847 ASP cc_start: 0.8881 (m-30) cc_final: 0.8561 (m-30) REVERT: A 2962 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7431 (pptt) REVERT: A 2994 MET cc_start: 0.8095 (mmm) cc_final: 0.7571 (mmm) REVERT: A 3030 MET cc_start: 0.8017 (mmm) cc_final: 0.7566 (mmp) REVERT: A 3039 LYS cc_start: 0.9358 (mmtm) cc_final: 0.8982 (ttmt) REVERT: A 3051 TYR cc_start: 0.8303 (t80) cc_final: 0.7974 (t80) REVERT: A 3199 MET cc_start: 0.7131 (mtp) cc_final: 0.6860 (tmm) REVERT: A 3586 TYR cc_start: 0.8343 (m-80) cc_final: 0.8038 (m-10) REVERT: A 3591 ASP cc_start: 0.7667 (t0) cc_final: 0.6722 (p0) REVERT: A 3615 LEU cc_start: 0.8927 (mt) cc_final: 0.8306 (pp) REVERT: A 3960 TRP cc_start: 0.8556 (t60) cc_final: 0.7874 (t60) REVERT: A 3991 LEU cc_start: 0.9245 (mt) cc_final: 0.8918 (mt) REVERT: A 4063 ASN cc_start: 0.8696 (t0) cc_final: 0.8447 (t0) REVERT: A 4195 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8255 (mtm110) REVERT: A 4296 MET cc_start: 0.8980 (tmm) cc_final: 0.8223 (tmm) REVERT: A 4462 ARG cc_start: 0.7373 (tpp80) cc_final: 0.7136 (tpp80) REVERT: A 4544 ASN cc_start: 0.8261 (t0) cc_final: 0.8001 (t0) REVERT: A 4604 VAL cc_start: 0.8525 (t) cc_final: 0.8152 (p) outliers start: 63 outliers final: 48 residues processed: 328 average time/residue: 0.3301 time to fit residues: 171.6328 Evaluate side-chains 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL 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 2084 SER 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 2273 ARG Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE 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 2846 THR Chi-restraints excluded: chain A residue 2946 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 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 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 3696 VAL 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 3933 GLU 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 4256 VAL Chi-restraints excluded: chain A residue 4274 THR 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 74 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS ** 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 = 0.3716 r_free = 0.3716 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079761 restraints weight = 64931.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082243 restraints weight = 34606.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083936 restraints weight = 23695.220| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22340 Z= 0.131 Angle : 0.623 17.449 30308 Z= 0.299 Chirality : 0.040 0.246 3412 Planarity : 0.004 0.047 3883 Dihedral : 6.075 159.245 3012 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.29 % Allowed : 21.69 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.16), residues: 2699 helix: 1.95 (0.13), residues: 1528 sheet: -0.72 (0.32), residues: 239 loop : 0.26 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A2584 HIS 0.007 0.001 HIS A1779 PHE 0.019 0.001 PHE A1870 TYR 0.021 0.001 TYR A4447 ARG 0.007 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1258) hydrogen bonds : angle 4.28156 ( 3675) covalent geometry : bond 0.00297 (22340) covalent geometry : angle 0.62326 (30308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 2.321 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: 0.5916 (mmm) cc_final: 0.5688 (mmp) REVERT: A 1798 MET cc_start: 0.8677 (mtm) cc_final: 0.8388 (ptp) REVERT: A 1892 MET cc_start: 0.9277 (mmt) cc_final: 0.9033 (mmm) REVERT: A 1937 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 1958 ASP cc_start: 0.8485 (t0) cc_final: 0.7832 (m-30) REVERT: A 1960 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 2099 SER cc_start: 0.9489 (m) cc_final: 0.8977 (p) REVERT: A 2130 ASN cc_start: 0.8870 (m110) cc_final: 0.8608 (p0) REVERT: A 2149 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 2220 LEU cc_start: 0.8831 (tp) cc_final: 0.8605 (tt) REVERT: A 2273 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6662 (ttp80) REVERT: A 2302 VAL cc_start: 0.9082 (t) cc_final: 0.8810 (m) REVERT: A 2493 TYR cc_start: 0.8508 (t80) cc_final: 0.7745 (t80) REVERT: A 2510 MET cc_start: 0.8425 (mpp) cc_final: 0.7947 (mtt) REVERT: A 2584 TRP cc_start: 0.8335 (m-90) cc_final: 0.7510 (m-90) REVERT: A 2615 MET cc_start: 0.7907 (ppp) cc_final: 0.7629 (ppp) REVERT: A 2717 ASP cc_start: 0.7534 (t70) cc_final: 0.7000 (p0) REVERT: A 2775 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: A 2799 MET cc_start: 0.7404 (ttm) cc_final: 0.6648 (ttm) REVERT: A 2847 ASP cc_start: 0.8843 (m-30) cc_final: 0.8536 (m-30) REVERT: A 2962 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7521 (pptt) REVERT: A 2994 MET cc_start: 0.8111 (mmm) cc_final: 0.7884 (tpp) REVERT: A 3030 MET cc_start: 0.8033 (mmm) cc_final: 0.7584 (mmm) REVERT: A 3039 LYS cc_start: 0.9379 (mmtm) cc_final: 0.9009 (ttmt) REVERT: A 3051 TYR cc_start: 0.8289 (t80) cc_final: 0.7982 (t80) REVERT: A 3199 MET cc_start: 0.7128 (mtp) cc_final: 0.6851 (tmm) REVERT: A 3586 TYR cc_start: 0.8365 (m-80) cc_final: 0.7963 (m-10) REVERT: A 3591 ASP cc_start: 0.7701 (t0) cc_final: 0.6753 (p0) REVERT: A 3615 LEU cc_start: 0.8918 (mt) cc_final: 0.8242 (pp) REVERT: A 3960 TRP cc_start: 0.8501 (t60) cc_final: 0.7776 (t60) REVERT: A 3991 LEU cc_start: 0.9288 (mt) cc_final: 0.8947 (mt) REVERT: A 4195 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8268 (mtm110) REVERT: A 4296 MET cc_start: 0.9003 (tmm) cc_final: 0.8164 (tmm) REVERT: A 4462 ARG cc_start: 0.7338 (tpp80) cc_final: 0.7117 (tpp80) REVERT: A 4544 ASN cc_start: 0.8241 (t0) cc_final: 0.8026 (t0) REVERT: A 4604 VAL cc_start: 0.8589 (t) cc_final: 0.8259 (p) outliers start: 55 outliers final: 46 residues processed: 310 average time/residue: 0.3210 time to fit residues: 159.5471 Evaluate side-chains 312 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL 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 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS Chi-restraints excluded: chain A residue 2261 LYS Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2731 VAL 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 2946 LEU Chi-restraints excluded: chain A residue 2990 ILE 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 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 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 3731 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 4055 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 4256 VAL Chi-restraints excluded: chain A residue 4274 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.077983 restraints weight = 65476.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080489 restraints weight = 35200.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082112 restraints weight = 24087.880| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22340 Z= 0.166 Angle : 0.651 14.228 30308 Z= 0.314 Chirality : 0.041 0.247 3412 Planarity : 0.004 0.055 3883 Dihedral : 6.214 160.152 3012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 21.94 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.16), residues: 2699 helix: 1.92 (0.13), residues: 1524 sheet: -0.72 (0.32), residues: 238 loop : 0.19 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A2584 HIS 0.007 0.001 HIS A1779 PHE 0.021 0.002 PHE A3496 TYR 0.019 0.001 TYR A2496 ARG 0.007 0.000 ARG A4449 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1258) hydrogen bonds : angle 4.33565 ( 3675) covalent geometry : bond 0.00379 (22340) covalent geometry : angle 0.65140 (30308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 2.413 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: 0.5697 (mmm) cc_final: 0.5483 (mmp) REVERT: A 1798 MET cc_start: 0.8718 (mtm) cc_final: 0.8453 (ptp) REVERT: A 1892 MET cc_start: 0.9233 (mmt) cc_final: 0.8989 (mmm) REVERT: A 1937 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 1958 ASP cc_start: 0.8552 (t0) cc_final: 0.7854 (m-30) REVERT: A 1960 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7622 (t80) REVERT: A 2099 SER cc_start: 0.9500 (m) cc_final: 0.9004 (p) REVERT: A 2130 ASN cc_start: 0.8879 (m110) cc_final: 0.8578 (p0) REVERT: A 2149 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8826 (tp) REVERT: A 2220 LEU cc_start: 0.8887 (tp) cc_final: 0.8682 (tt) REVERT: A 2273 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6747 (ttp80) REVERT: A 2302 VAL cc_start: 0.9211 (t) cc_final: 0.8940 (m) REVERT: A 2313 GLU cc_start: 0.8282 (pp20) cc_final: 0.7537 (mp0) REVERT: A 2346 GLN cc_start: 0.7660 (pt0) cc_final: 0.7420 (pt0) REVERT: A 2510 MET cc_start: 0.8425 (mpp) cc_final: 0.7768 (mtt) REVERT: A 2584 TRP cc_start: 0.8351 (m-90) cc_final: 0.7438 (m-90) REVERT: A 2717 ASP cc_start: 0.7548 (t70) cc_final: 0.6893 (p0) REVERT: A 2720 ARG cc_start: 0.5664 (mmt-90) cc_final: 0.4818 (mpt180) REVERT: A 2847 ASP cc_start: 0.8832 (m-30) cc_final: 0.8499 (m-30) REVERT: A 2962 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7689 (pptt) REVERT: A 3030 MET cc_start: 0.8036 (mmm) cc_final: 0.7604 (mmp) REVERT: A 3039 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9004 (ttmt) REVERT: A 3051 TYR cc_start: 0.8253 (t80) cc_final: 0.7931 (t80) REVERT: A 3199 MET cc_start: 0.7118 (mtp) cc_final: 0.6826 (tmm) REVERT: A 3500 MET cc_start: 0.7626 (mmm) cc_final: 0.7336 (mmm) REVERT: A 3586 TYR cc_start: 0.8431 (m-80) cc_final: 0.8176 (m-10) REVERT: A 3591 ASP cc_start: 0.7717 (t0) cc_final: 0.6739 (p0) REVERT: A 3615 LEU cc_start: 0.8913 (mt) cc_final: 0.8230 (pp) REVERT: A 3960 TRP cc_start: 0.8538 (t60) cc_final: 0.7809 (t60) REVERT: A 4195 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8299 (mtm110) REVERT: A 4296 MET cc_start: 0.9032 (tmm) cc_final: 0.8204 (tmm) outliers start: 59 outliers final: 50 residues processed: 299 average time/residue: 0.3262 time to fit residues: 157.5677 Evaluate side-chains 301 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL 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 1967 MET Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2186 CYS 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 2345 VAL Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2534 ILE 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 2846 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 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 3589 ILE Chi-restraints excluded: chain A residue 3640 SER 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 3900 THR Chi-restraints excluded: chain A residue 3933 GLU 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 4256 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 4618 LEU 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 49 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3672 r_free = 0.3672 target = 0.102887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076929 restraints weight = 65606.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079391 restraints weight = 35599.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080969 restraints weight = 24421.137| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22340 Z= 0.181 Angle : 0.670 14.436 30308 Z= 0.325 Chirality : 0.042 0.246 3412 Planarity : 0.004 0.072 3883 Dihedral : 6.210 162.105 3012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.33 % Allowed : 22.31 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.16), residues: 2699 helix: 1.87 (0.13), residues: 1522 sheet: -0.74 (0.32), residues: 231 loop : 0.16 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A2584 HIS 0.008 0.001 HIS A4187 PHE 0.022 0.002 PHE A3496 TYR 0.020 0.002 TYR A2496 ARG 0.004 0.000 ARG A2358 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1258) hydrogen bonds : angle 4.38644 ( 3675) covalent geometry : bond 0.00415 (22340) covalent geometry : angle 0.66960 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.08 seconds wall clock time: 131 minutes 32.15 seconds (7892.15 seconds total)