Starting phenix.real_space_refine on Thu Jun 19 08:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmo_44705/06_2025/9bmo_44705.cif" } resolution = 3.6 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= 0.038 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 95 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.32, per 1000 atoms: 0.52 Number of scatterers: 21867 At special positions: 0 Unit cell: (148.428, 162.75, 121.086, 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: 5.16 Conformation dependent library (CDL) restraints added in 2.5 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 17 sheets defined 61.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.693A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.576A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1841 removed outlier: 4.204A 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 1924 Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.713A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.708A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.587A 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 2129 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: 4.304A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.794A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.694A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.553A 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: 3.815A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.583A 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 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.859A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.724A pdb=" N ARG A2576 " --> pdb=" O LEU A2572 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.543A pdb=" N ALA A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.941A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2731 removed outlier: 3.929A pdb=" N HIS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 4.235A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.869A pdb=" N LEU A2762 " --> pdb=" O ILE A2759 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.822A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.560A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.679A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3087 removed outlier: 3.508A pdb=" N PHE A3086 " --> pdb=" O PRO A3083 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.590A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 3.613A pdb=" N PHE A3496 " --> pdb=" O THR A3492 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 4.020A 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: 3.872A 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 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 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 3735 removed outlier: 3.783A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A3732 " --> pdb=" O ARG A3728 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A3733 " --> pdb=" O SER A3729 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3755 Processing helix chain 'A' and resid 3763 through 3793 removed outlier: 4.075A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3819 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.560A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3917 through 3921 Processing helix chain 'A' and resid 3928 through 3940 Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.949A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4019 removed outlier: 4.475A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.635A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.784A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.024A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.678A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.614A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.624A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.396A 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: 3.776A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.509A 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 4457 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 4.235A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.516A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 4.090A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.847A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A2017 " --> pdb=" O PHE A1957 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A1959 " --> pdb=" O THR A2017 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 8.012A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 removed outlier: 3.695A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) 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: 6.431A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A2734 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 3.658A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.265A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 3.523A pdb=" N LEU A3634 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.342A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.597A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A4589 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 3.624A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1251 hydrogen bonds defined for protein. 3669 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: 11.71 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7207 1.34 - 1.46: 4933 1.46 - 1.58: 10000 1.58 - 1.70: 15 1.70 - 1.82: 185 Bond restraints: 22340 Sorted by residual: bond pdb=" CB PRO A4132 " pdb=" CG PRO A4132 " ideal model delta sigma weight residual 1.492 1.647 -0.155 5.00e-02 4.00e+02 9.62e+00 bond pdb=" CG PRO A4132 " pdb=" CD PRO A4132 " ideal model delta sigma weight residual 1.503 1.411 0.092 3.40e-02 8.65e+02 7.26e+00 bond pdb=" CB PRO A2929 " pdb=" CG PRO A2929 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.83e+00 bond pdb=" N PRO A4132 " pdb=" CD PRO A4132 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.59e+00 bond pdb=" N PRO A4132 " pdb=" CA PRO A4132 " ideal model delta sigma weight residual 1.471 1.448 0.023 1.32e-02 5.74e+03 3.06e+00 ... (remaining 22335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 30131 3.48 - 6.96: 162 6.96 - 10.44: 12 10.44 - 13.93: 2 13.93 - 17.41: 1 Bond angle restraints: 30308 Sorted by residual: angle pdb=" CA PRO A4132 " pdb=" N PRO A4132 " pdb=" CD PRO A4132 " ideal model delta sigma weight residual 112.00 94.59 17.41 1.40e+00 5.10e-01 1.55e+02 angle pdb=" N PRO A4132 " pdb=" CD PRO A4132 " pdb=" CG PRO A4132 " ideal model delta sigma weight residual 103.20 94.04 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" CA PRO A2929 " pdb=" N PRO A2929 " pdb=" CD PRO A2929 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" CB MET A4021 " pdb=" CG MET A4021 " pdb=" SD MET A4021 " ideal model delta sigma weight residual 112.70 124.72 -12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA PRO A4132 " pdb=" CB PRO A4132 " pdb=" CG PRO A4132 " ideal model delta sigma weight residual 104.50 97.59 6.91 1.90e+00 2.77e-01 1.32e+01 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.50: 12681 28.50 - 57.00: 762 57.00 - 85.50: 92 85.50 - 114.00: 6 114.00 - 142.50: 1 Dihedral angle restraints: 13542 sinusoidal: 5612 harmonic: 7930 Sorted by residual: dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 157.50 142.50 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O1B ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PB ADP A4703 " pdb=" PA ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 44.46 -104.46 1 2.00e+01 2.50e-03 3.00e+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 33.77 -93.78 1 2.00e+01 2.50e-03 2.56e+01 ... (remaining 13539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2680 0.046 - 0.092: 564 0.092 - 0.138: 158 0.138 - 0.184: 9 0.184 - 0.230: 1 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CB ILE A1944 " pdb=" CA ILE A1944 " pdb=" CG1 ILE A1944 " pdb=" CG2 ILE A1944 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A4212 " pdb=" CB LEU A4212 " pdb=" CD1 LEU A4212 " pdb=" CD2 LEU A4212 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CG LEU A2097 " pdb=" CB LEU A2097 " pdb=" CD1 LEU A2097 " pdb=" CD2 LEU A2097 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 3409 not shown) Planarity restraints: 3883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A4131 " -0.110 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO A4132 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO A4132 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO A4132 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A3135 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A3136 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A3136 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A3136 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2335 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A2336 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A2336 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A2336 " 0.048 5.00e-02 4.00e+02 ... (remaining 3880 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 434 2.68 - 3.24: 22458 3.24 - 3.79: 36386 3.79 - 4.35: 45823 4.35 - 4.90: 74503 Nonbonded interactions: 179604 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 2.126 3.040 nonbonded pdb=" OD2 ASP A2269 " pdb=" OG1 THR A2272 " model vdw 2.162 3.040 nonbonded pdb=" O ALA A2497 " pdb=" OG SER A2501 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR A2748 " pdb=" OG1 THR A2800 " model vdw 2.187 3.040 nonbonded pdb=" O LEU A1968 " pdb=" OG SER A1972 " model vdw 2.196 3.040 ... (remaining 179599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 51.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 22340 Z= 0.146 Angle : 0.675 17.406 30308 Z= 0.349 Chirality : 0.041 0.230 3412 Planarity : 0.005 0.151 3883 Dihedral : 17.435 142.502 8390 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.46 % Allowed : 23.39 % 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: 1.30 (0.16), residues: 2699 helix: 1.80 (0.13), residues: 1501 sheet: -0.92 (0.36), residues: 208 loop : -0.11 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A4376 HIS 0.008 0.001 HIS A4466 PHE 0.043 0.002 PHE A2972 TYR 0.041 0.002 TYR A4636 ARG 0.010 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.13977 ( 1251) hydrogen bonds : angle 5.98997 ( 3669) covalent geometry : bond 0.00341 (22340) covalent geometry : angle 0.67460 (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 261 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1925 ARG cc_start: 0.7714 (mmt90) cc_final: 0.7116 (mmt90) REVERT: A 2510 MET cc_start: 0.7532 (ttp) cc_final: 0.7314 (ttm) REVERT: A 2615 MET cc_start: 0.7417 (pmm) cc_final: 0.7139 (pmm) REVERT: A 2799 MET cc_start: 0.7856 (mmm) cc_final: 0.7427 (tpp) REVERT: A 3078 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6403 (mtt90) REVERT: A 3113 MET cc_start: 0.6447 (mpp) cc_final: 0.5691 (tpt) REVERT: A 4192 GLU cc_start: 0.7720 (mp0) cc_final: 0.7256 (mp0) outliers start: 11 outliers final: 7 residues processed: 255 average time/residue: 0.3341 time to fit residues: 134.9693 Evaluate side-chains 235 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4509 VAL 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: 8.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS ** A2271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2730 HIS A2857 HIS A2998 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS A3906 GLN A3988 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095516 restraints weight = 49553.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097379 restraints weight = 27739.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099835 restraints weight = 19008.679| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22340 Z= 0.235 Angle : 0.662 8.487 30308 Z= 0.333 Chirality : 0.043 0.158 3412 Planarity : 0.005 0.077 3883 Dihedral : 7.372 135.777 3026 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.45 % Allowed : 20.57 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.16), residues: 2699 helix: 1.62 (0.13), residues: 1524 sheet: -1.20 (0.32), residues: 235 loop : -0.02 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2584 HIS 0.006 0.001 HIS A3151 PHE 0.024 0.002 PHE A1727 TYR 0.023 0.002 TYR A2901 ARG 0.005 0.001 ARG A4176 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1251) hydrogen bonds : angle 4.92535 ( 3669) covalent geometry : bond 0.00545 (22340) covalent geometry : angle 0.66156 (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 328 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 245 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8750 (m-10) cc_final: 0.8469 (m-10) REVERT: A 2012 MET cc_start: 0.8412 (tpp) cc_final: 0.7949 (tpp) REVERT: A 2231 SER cc_start: 0.7425 (OUTLIER) cc_final: 0.5702 (p) REVERT: A 2582 TYR cc_start: 0.8009 (t80) cc_final: 0.7733 (t80) REVERT: A 2585 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9118 (mm) REVERT: A 2670 ASP cc_start: 0.7029 (p0) cc_final: 0.6615 (p0) REVERT: A 2721 LYS cc_start: 0.8731 (mppt) cc_final: 0.8172 (mtmm) REVERT: A 2799 MET cc_start: 0.8137 (mmm) cc_final: 0.7714 (tpp) REVERT: A 2926 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 3104 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 3113 MET cc_start: 0.6719 (mpp) cc_final: 0.5777 (tpt) REVERT: A 3684 PRO cc_start: 0.9134 (Cg_endo) cc_final: 0.8878 (Cg_exo) REVERT: A 4192 GLU cc_start: 0.8006 (mp0) cc_final: 0.7720 (mp0) outliers start: 83 outliers final: 46 residues processed: 313 average time/residue: 0.3278 time to fit residues: 162.3644 Evaluate side-chains 266 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2412 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2903 GLU Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2947 SER Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4389 HIS Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 139 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 193 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2857 HIS A3139 HIS ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3538 GLN A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.123580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098685 restraints weight = 48698.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100986 restraints weight = 26352.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102812 restraints weight = 17147.716| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22340 Z= 0.122 Angle : 0.568 9.093 30308 Z= 0.281 Chirality : 0.040 0.163 3412 Planarity : 0.004 0.058 3883 Dihedral : 6.935 131.420 3017 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.20 % Allowed : 22.60 % Favored : 75.20 % 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: 1.35 (0.16), residues: 2699 helix: 1.78 (0.13), residues: 1527 sheet: -0.92 (0.34), residues: 207 loop : -0.00 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4376 HIS 0.003 0.001 HIS A2263 PHE 0.029 0.001 PHE A1727 TYR 0.018 0.001 TYR A4636 ARG 0.006 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1251) hydrogen bonds : angle 4.58648 ( 3669) covalent geometry : bond 0.00268 (22340) covalent geometry : angle 0.56750 (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 304 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8652 (m-10) cc_final: 0.8405 (m-10) REVERT: A 1925 ARG cc_start: 0.7746 (mmt90) cc_final: 0.7177 (mmt90) REVERT: A 1966 ARG cc_start: 0.8171 (tpm170) cc_final: 0.7948 (tpm170) REVERT: A 2012 MET cc_start: 0.8433 (tpp) cc_final: 0.7964 (tpp) REVERT: A 2231 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.5178 (p) REVERT: A 2500 TRP cc_start: 0.8691 (m100) cc_final: 0.8401 (m100) REVERT: A 2551 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7985 (mptt) REVERT: A 2582 TYR cc_start: 0.7899 (t80) cc_final: 0.7653 (t80) REVERT: A 2670 ASP cc_start: 0.6956 (p0) cc_final: 0.6547 (p0) REVERT: A 2688 GLU cc_start: 0.7922 (tt0) cc_final: 0.7682 (tt0) REVERT: A 2721 LYS cc_start: 0.8789 (mppt) cc_final: 0.8309 (mtmm) REVERT: A 2755 MET cc_start: 0.6715 (tmm) cc_final: 0.6408 (tmm) REVERT: A 2799 MET cc_start: 0.7919 (mmm) cc_final: 0.7457 (tpp) REVERT: A 3008 MET cc_start: 0.8433 (tpp) cc_final: 0.7500 (ttp) REVERT: A 3104 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: A 3113 MET cc_start: 0.6729 (mpp) cc_final: 0.5827 (tpt) REVERT: A 3620 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8368 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9105 (Cg_endo) cc_final: 0.8852 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7490 (tp40) REVERT: A 4095 MET cc_start: 0.7523 (mmm) cc_final: 0.7202 (mmm) REVERT: A 4133 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7601 (ttpp) REVERT: A 4192 GLU cc_start: 0.8042 (mp0) cc_final: 0.7764 (mp0) outliers start: 53 outliers final: 27 residues processed: 297 average time/residue: 0.3576 time to fit residues: 167.8597 Evaluate side-chains 252 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 260 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2707 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.120254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094956 restraints weight = 50505.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096869 restraints weight = 28136.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099086 restraints weight = 18708.755| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22340 Z= 0.212 Angle : 0.622 12.791 30308 Z= 0.310 Chirality : 0.042 0.162 3412 Planarity : 0.005 0.097 3883 Dihedral : 7.108 140.437 3016 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.41 % Allowed : 22.39 % Favored : 74.20 % 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: 1.23 (0.16), residues: 2699 helix: 1.69 (0.13), residues: 1525 sheet: -1.24 (0.33), residues: 232 loop : 0.05 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2234 HIS 0.006 0.001 HIS A2560 PHE 0.027 0.002 PHE A1727 TYR 0.020 0.002 TYR A3516 ARG 0.014 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 1251) hydrogen bonds : angle 4.59999 ( 3669) covalent geometry : bond 0.00493 (22340) covalent geometry : angle 0.62175 (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 323 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 241 time to evaluate : 2.669 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: A 1704 LEU cc_start: 0.8897 (mt) cc_final: 0.8693 (mt) REVERT: A 1889 TYR cc_start: 0.8738 (m-10) cc_final: 0.8499 (m-10) REVERT: A 1966 ARG cc_start: 0.8214 (tpm170) cc_final: 0.7748 (tpm170) REVERT: A 2012 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7230 (tpp) REVERT: A 2231 SER cc_start: 0.7156 (OUTLIER) cc_final: 0.5355 (p) REVERT: A 2496 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 2510 MET cc_start: 0.7378 (ttt) cc_final: 0.7047 (ttt) REVERT: A 2551 LYS cc_start: 0.8286 (mmtp) cc_final: 0.8039 (mptt) REVERT: A 2670 ASP cc_start: 0.7001 (p0) cc_final: 0.6571 (p0) REVERT: A 2721 LYS cc_start: 0.8833 (mppt) cc_final: 0.8329 (mtmm) REVERT: A 2755 MET cc_start: 0.6555 (tmm) cc_final: 0.6216 (tmm) REVERT: A 2799 MET cc_start: 0.8024 (mmm) cc_final: 0.7607 (tpp) REVERT: A 2926 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: A 2966 LYS cc_start: 0.8699 (tptt) cc_final: 0.8327 (mmtt) REVERT: A 3104 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: A 3113 MET cc_start: 0.7003 (mpp) cc_final: 0.6140 (tpt) REVERT: A 3684 PRO cc_start: 0.9113 (Cg_endo) cc_final: 0.8847 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7518 (tp40) REVERT: A 3983 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 4133 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7675 (ttpp) REVERT: A 4192 GLU cc_start: 0.8061 (mp0) cc_final: 0.7690 (mp0) REVERT: A 4635 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8618 (m-80) outliers start: 82 outliers final: 50 residues processed: 307 average time/residue: 0.3599 time to fit residues: 172.5974 Evaluate side-chains 277 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 258 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2707 GLN A2827 HIS ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3555 ASN A3852 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095915 restraints weight = 49926.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098070 restraints weight = 27584.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100134 restraints weight = 18044.961| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1831 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= 0.158 Angle : 0.582 9.138 30308 Z= 0.289 Chirality : 0.040 0.188 3412 Planarity : 0.004 0.075 3883 Dihedral : 7.136 170.907 3016 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.32 % Allowed : 22.64 % Favored : 74.03 % 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: 1.26 (0.16), residues: 2699 helix: 1.71 (0.13), residues: 1531 sheet: -1.09 (0.34), residues: 216 loop : -0.01 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.007 0.001 HIS A2560 PHE 0.025 0.002 PHE A1727 TYR 0.017 0.001 TYR A3516 ARG 0.008 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1251) hydrogen bonds : angle 4.46206 ( 3669) covalent geometry : bond 0.00365 (22340) covalent geometry : angle 0.58168 (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 325 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 245 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8855 (mt) cc_final: 0.8638 (mt) REVERT: A 1889 TYR cc_start: 0.8708 (m-10) cc_final: 0.8467 (m-10) REVERT: A 1966 ARG cc_start: 0.8232 (tpm170) cc_final: 0.7697 (tpm170) REVERT: A 1974 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8604 (mm-40) REVERT: A 2231 SER cc_start: 0.6881 (OUTLIER) cc_final: 0.6206 (m) REVERT: A 2422 ILE cc_start: 0.8250 (mm) cc_final: 0.7971 (mm) REVERT: A 2496 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7552 (t80) REVERT: A 2510 MET cc_start: 0.7792 (ttt) cc_final: 0.7364 (ttt) REVERT: A 2585 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9227 (mm) REVERT: A 2721 LYS cc_start: 0.8765 (mppt) cc_final: 0.8540 (ptpp) REVERT: A 2755 MET cc_start: 0.6633 (tmm) cc_final: 0.6253 (tmm) REVERT: A 2799 MET cc_start: 0.7991 (mmm) cc_final: 0.7587 (tpp) REVERT: A 2926 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8598 (m-10) REVERT: A 3008 MET cc_start: 0.8120 (tpp) cc_final: 0.7235 (ttp) REVERT: A 3104 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: A 3113 MET cc_start: 0.7194 (mpp) cc_final: 0.6271 (tpt) REVERT: A 3684 PRO cc_start: 0.9095 (Cg_endo) cc_final: 0.8822 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: A 4133 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7620 (ttpp) REVERT: A 4192 GLU cc_start: 0.8036 (mp0) cc_final: 0.7692 (mp0) REVERT: A 4635 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8568 (m-80) outliers start: 80 outliers final: 47 residues processed: 313 average time/residue: 0.5169 time to fit residues: 258.5448 Evaluate side-chains 281 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 6 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A3845 ASN A3852 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096446 restraints weight = 49388.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098767 restraints weight = 27800.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101634 restraints weight = 17889.648| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.141 Angle : 0.572 8.417 30308 Z= 0.284 Chirality : 0.040 0.184 3412 Planarity : 0.004 0.064 3883 Dihedral : 6.710 156.661 3014 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.28 % Allowed : 23.02 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.16), residues: 2699 helix: 1.75 (0.13), residues: 1532 sheet: -1.05 (0.33), residues: 224 loop : -0.02 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2825 HIS 0.005 0.001 HIS A2560 PHE 0.033 0.002 PHE A1727 TYR 0.014 0.001 TYR A3516 ARG 0.005 0.000 ARG A1623 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 1251) hydrogen bonds : angle 4.38383 ( 3669) covalent geometry : bond 0.00323 (22340) covalent geometry : angle 0.57176 (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 316 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 237 time to evaluate : 3.581 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: A 1704 LEU cc_start: 0.8776 (mt) cc_final: 0.8559 (mt) REVERT: A 1889 TYR cc_start: 0.8753 (m-10) cc_final: 0.8533 (m-10) REVERT: A 1966 ARG cc_start: 0.8156 (tpm170) cc_final: 0.7540 (tpm170) REVERT: A 2012 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7343 (tpp) REVERT: A 2231 SER cc_start: 0.6886 (OUTLIER) cc_final: 0.6550 (m) REVERT: A 2496 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 2510 MET cc_start: 0.7746 (ttt) cc_final: 0.7451 (ttt) REVERT: A 2670 ASP cc_start: 0.6742 (p0) cc_final: 0.6368 (p0) REVERT: A 2799 MET cc_start: 0.7921 (mmm) cc_final: 0.7514 (tpp) REVERT: A 2825 TRP cc_start: 0.8531 (t60) cc_final: 0.8031 (t60) REVERT: A 2926 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: A 2966 LYS cc_start: 0.8649 (tptt) cc_final: 0.8290 (mmtt) REVERT: A 3008 MET cc_start: 0.8185 (tpp) cc_final: 0.7295 (ttp) REVERT: A 3104 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: A 3620 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8261 (mmm160) REVERT: A 3684 PRO cc_start: 0.9073 (Cg_endo) cc_final: 0.8787 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7526 (tp40) REVERT: A 4133 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7619 (ttpp) REVERT: A 4171 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8477 (mmmm) REVERT: A 4192 GLU cc_start: 0.7965 (mp0) cc_final: 0.7027 (mp0) REVERT: A 4635 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8492 (m-80) outliers start: 79 outliers final: 55 residues processed: 301 average time/residue: 0.5587 time to fit residues: 274.0773 Evaluate side-chains 280 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 5 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2485 GLN A2857 HIS A3852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097578 restraints weight = 49675.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099774 restraints weight = 27448.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101548 restraints weight = 17965.457| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22340 Z= 0.152 Angle : 0.580 10.184 30308 Z= 0.287 Chirality : 0.041 0.236 3412 Planarity : 0.004 0.056 3883 Dihedral : 6.235 125.424 3014 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.78 % Allowed : 22.97 % Favored : 73.24 % 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: 1.32 (0.16), residues: 2699 helix: 1.77 (0.13), residues: 1529 sheet: -1.04 (0.33), residues: 225 loop : -0.01 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.005 0.001 HIS A2560 PHE 0.034 0.002 PHE A1727 TYR 0.014 0.001 TYR A3516 ARG 0.006 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 1251) hydrogen bonds : angle 4.35367 ( 3669) covalent geometry : bond 0.00350 (22340) covalent geometry : angle 0.57966 (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 314 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 223 time to evaluate : 2.722 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: A 1704 LEU cc_start: 0.8809 (mt) cc_final: 0.8590 (mt) REVERT: A 1889 TYR cc_start: 0.8639 (m-10) cc_final: 0.8404 (m-10) REVERT: A 1966 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7547 (tpm170) REVERT: A 2231 SER cc_start: 0.6776 (OUTLIER) cc_final: 0.6134 (m) REVERT: A 2361 MET cc_start: 0.8503 (ttm) cc_final: 0.8110 (ttm) REVERT: A 2496 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 2510 MET cc_start: 0.7856 (ttm) cc_final: 0.7384 (ttt) REVERT: A 2671 MET cc_start: 0.7608 (mmm) cc_final: 0.7276 (mmm) REVERT: A 2755 MET cc_start: 0.7106 (tmm) cc_final: 0.6782 (tmm) REVERT: A 2799 MET cc_start: 0.7938 (mmm) cc_final: 0.7544 (tpp) REVERT: A 2825 TRP cc_start: 0.8593 (t60) cc_final: 0.8123 (t60) REVERT: A 3008 MET cc_start: 0.8158 (tpp) cc_final: 0.7147 (ttp) REVERT: A 3088 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7034 (ttm-80) REVERT: A 3104 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: A 3620 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8256 (mmm160) REVERT: A 3684 PRO cc_start: 0.9067 (Cg_endo) cc_final: 0.8781 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7586 (tp40) REVERT: A 4133 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7679 (ttpp) REVERT: A 4171 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8492 (mmmm) REVERT: A 4192 GLU cc_start: 0.8009 (mp0) cc_final: 0.7692 (mp0) REVERT: A 4635 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8518 (m-80) outliers start: 91 outliers final: 67 residues processed: 294 average time/residue: 0.3895 time to fit residues: 185.0383 Evaluate side-chains 290 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4334 THR Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 131 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 264 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2928 GLN A3852 HIS A4477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096784 restraints weight = 49939.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099293 restraints weight = 27912.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101410 restraints weight = 17814.778| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22340 Z= 0.154 Angle : 0.581 9.735 30308 Z= 0.288 Chirality : 0.041 0.246 3412 Planarity : 0.004 0.055 3883 Dihedral : 5.754 106.041 3014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.41 % Allowed : 23.76 % Favored : 72.83 % 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: 1.32 (0.16), residues: 2699 helix: 1.76 (0.13), residues: 1534 sheet: -0.99 (0.34), residues: 224 loop : -0.01 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A2560 PHE 0.036 0.002 PHE A1727 TYR 0.014 0.001 TYR A2967 ARG 0.004 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1251) hydrogen bonds : angle 4.31546 ( 3669) covalent geometry : bond 0.00355 (22340) covalent geometry : angle 0.58118 (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 307 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 225 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8815 (mt) cc_final: 0.8586 (mt) REVERT: A 1966 ARG cc_start: 0.8213 (tpm170) cc_final: 0.7579 (tpm170) REVERT: A 2012 MET cc_start: 0.8573 (tmm) cc_final: 0.8326 (tmm) REVERT: A 2231 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6503 (m) REVERT: A 2369 LEU cc_start: 0.8906 (mt) cc_final: 0.8415 (mt) REVERT: A 2496 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 2510 MET cc_start: 0.7845 (ttm) cc_final: 0.7370 (ttt) REVERT: A 2610 ARG cc_start: 0.7371 (ppt170) cc_final: 0.7136 (ppt170) REVERT: A 2671 MET cc_start: 0.7632 (mmm) cc_final: 0.7293 (mmm) REVERT: A 2755 MET cc_start: 0.7081 (tmm) cc_final: 0.6738 (tmm) REVERT: A 2799 MET cc_start: 0.7945 (mmm) cc_final: 0.7561 (tpp) REVERT: A 2825 TRP cc_start: 0.8582 (t60) cc_final: 0.8113 (t60) REVERT: A 3104 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: A 3113 MET cc_start: 0.6837 (mpp) cc_final: 0.6576 (mpp) REVERT: A 3620 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8278 (mmm160) REVERT: A 3684 PRO cc_start: 0.9097 (Cg_endo) cc_final: 0.8789 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7532 (tp40) REVERT: A 4133 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7693 (ttpp) REVERT: A 4171 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (mmmm) REVERT: A 4192 GLU cc_start: 0.7965 (mp0) cc_final: 0.7619 (mp0) REVERT: A 4457 LYS cc_start: 0.8535 (tppt) cc_final: 0.7689 (ptpt) REVERT: A 4635 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8478 (m-80) outliers start: 82 outliers final: 64 residues processed: 288 average time/residue: 0.3561 time to fit residues: 164.6388 Evaluate side-chains 291 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4334 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 257 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A3852 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101490 restraints weight = 50968.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105030 restraints weight = 27164.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105987 restraints weight = 16104.670| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.146 Angle : 0.591 12.630 30308 Z= 0.292 Chirality : 0.041 0.294 3412 Planarity : 0.004 0.076 3883 Dihedral : 5.542 106.872 3014 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.12 % Allowed : 24.22 % Favored : 72.66 % 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: 1.35 (0.16), residues: 2699 helix: 1.79 (0.13), residues: 1526 sheet: -0.89 (0.34), residues: 216 loop : -0.02 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A2560 PHE 0.036 0.001 PHE A1727 TYR 0.013 0.001 TYR A3516 ARG 0.014 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1251) hydrogen bonds : angle 4.29942 ( 3669) covalent geometry : bond 0.00337 (22340) covalent geometry : angle 0.59117 (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 305 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8779 (mt) cc_final: 0.8522 (mt) REVERT: A 1966 ARG cc_start: 0.8249 (tpm170) cc_final: 0.7565 (tpm170) REVERT: A 2012 MET cc_start: 0.8672 (tmm) cc_final: 0.8430 (tmm) REVERT: A 2231 SER cc_start: 0.6491 (OUTLIER) cc_final: 0.5866 (m) REVERT: A 2369 LEU cc_start: 0.8876 (mt) cc_final: 0.8339 (mt) REVERT: A 2496 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 2510 MET cc_start: 0.7927 (ttm) cc_final: 0.7557 (ttt) REVERT: A 2610 ARG cc_start: 0.7346 (ppt170) cc_final: 0.7101 (ppt170) REVERT: A 2671 MET cc_start: 0.7591 (mmm) cc_final: 0.7211 (mmm) REVERT: A 2755 MET cc_start: 0.7104 (tmm) cc_final: 0.6767 (tmm) REVERT: A 2799 MET cc_start: 0.8006 (mmm) cc_final: 0.7600 (tpp) REVERT: A 2825 TRP cc_start: 0.8578 (t60) cc_final: 0.8125 (t60) REVERT: A 2953 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6803 (tmm) REVERT: A 3008 MET cc_start: 0.8392 (tpp) cc_final: 0.7572 (ttp) REVERT: A 3088 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6873 (ttm170) REVERT: A 3104 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: A 3113 MET cc_start: 0.6792 (mpp) cc_final: 0.6560 (mpp) REVERT: A 3620 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8256 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9092 (Cg_endo) cc_final: 0.8764 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7293 (tp40) REVERT: A 4171 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (mmmm) REVERT: A 4192 GLU cc_start: 0.8033 (mp0) cc_final: 0.7062 (mp0) REVERT: A 4457 LYS cc_start: 0.8524 (tppt) cc_final: 0.7650 (ptpt) REVERT: A 4635 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8497 (m-80) outliers start: 75 outliers final: 60 residues processed: 288 average time/residue: 0.3482 time to fit residues: 160.1265 Evaluate side-chains 284 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2661 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3856 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4334 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 248 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1841 GLN A2263 HIS A2998 ASN A3852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.128044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100403 restraints weight = 51051.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103666 restraints weight = 25984.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105883 restraints weight = 17075.620| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22340 Z= 0.139 Angle : 0.590 11.728 30308 Z= 0.290 Chirality : 0.041 0.303 3412 Planarity : 0.004 0.066 3883 Dihedral : 5.535 107.783 3014 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 24.30 % Favored : 72.62 % 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: 1.38 (0.17), residues: 2699 helix: 1.80 (0.13), residues: 1526 sheet: -0.83 (0.35), residues: 216 loop : 0.01 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A2560 PHE 0.037 0.001 PHE A1727 TYR 0.012 0.001 TYR A3516 ARG 0.010 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1251) hydrogen bonds : angle 4.27286 ( 3669) covalent geometry : bond 0.00321 (22340) covalent geometry : angle 0.59022 (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 301 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8833 (mt) cc_final: 0.8597 (mt) REVERT: A 1925 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7597 (mmt90) REVERT: A 1966 ARG cc_start: 0.8252 (tpm170) cc_final: 0.7736 (tpm170) REVERT: A 2012 MET cc_start: 0.8711 (tmm) cc_final: 0.8508 (tmm) REVERT: A 2231 SER cc_start: 0.6800 (OUTLIER) cc_final: 0.6228 (m) REVERT: A 2369 LEU cc_start: 0.8911 (mt) cc_final: 0.8303 (mt) REVERT: A 2496 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 2510 MET cc_start: 0.7973 (ttm) cc_final: 0.7584 (ttt) REVERT: A 2610 ARG cc_start: 0.7414 (ppt170) cc_final: 0.7108 (ppt170) REVERT: A 2671 MET cc_start: 0.7638 (mmm) cc_final: 0.7265 (mmm) REVERT: A 2755 MET cc_start: 0.7116 (tmm) cc_final: 0.6777 (tmm) REVERT: A 2799 MET cc_start: 0.7961 (mmm) cc_final: 0.7562 (tpp) REVERT: A 2825 TRP cc_start: 0.8622 (t60) cc_final: 0.8166 (t60) REVERT: A 2953 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6781 (tmm) REVERT: A 3008 MET cc_start: 0.8263 (tpp) cc_final: 0.7464 (ttp) REVERT: A 3088 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.6946 (ttm170) REVERT: A 3104 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: A 3620 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8240 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9082 (Cg_endo) cc_final: 0.8767 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7272 (tp40) REVERT: A 4171 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8464 (mmmm) REVERT: A 4192 GLU cc_start: 0.7971 (mp0) cc_final: 0.7049 (mp0) REVERT: A 4457 LYS cc_start: 0.8492 (tppt) cc_final: 0.7647 (ptpt) REVERT: A 4635 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8479 (m-80) outliers start: 74 outliers final: 63 residues processed: 288 average time/residue: 0.4564 time to fit residues: 215.3600 Evaluate side-chains 291 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2661 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4334 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4578 SER Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4635 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 0.0020 chunk 74 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 252 optimal weight: 0.1980 chunk 155 optimal weight: 7.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2263 HIS A2857 HIS A3852 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102681 restraints weight = 50768.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105999 restraints weight = 25594.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108209 restraints weight = 16636.059| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22340 Z= 0.114 Angle : 0.587 11.915 30308 Z= 0.288 Chirality : 0.040 0.290 3412 Planarity : 0.004 0.056 3883 Dihedral : 5.426 109.493 3014 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.16 % Allowed : 25.26 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2699 helix: 1.88 (0.13), residues: 1527 sheet: -0.67 (0.36), residues: 206 loop : 0.04 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2825 HIS 0.004 0.001 HIS A2560 PHE 0.044 0.001 PHE A2682 TYR 0.014 0.001 TYR A3120 ARG 0.008 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 1251) hydrogen bonds : angle 4.18506 ( 3669) covalent geometry : bond 0.00254 (22340) covalent geometry : angle 0.58666 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7340.63 seconds wall clock time: 133 minutes 0.58 seconds (7980.58 seconds total)