Starting phenix.real_space_refine on Fri Sep 19 02:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmo_44705/09_2025/9bmo_44705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmo_44705/09_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_44705/09_2025/9bmo_44705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmo_44705/09_2025/9bmo_44705.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmo_44705/09_2025/9bmo_44705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmo_44705/09_2025/9bmo_44705.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.16, per 1000 atoms: 0.24 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 17 sheets defined 61.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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: 6.33 Time building geometry restraints manager: 2.57 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:1.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- 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 : 14.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.16), residues: 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 ARG 0.010 0.000 ARG A4263 TYR 0.041 0.002 TYR A4636 PHE 0.043 0.002 PHE A2972 TRP 0.036 0.002 TRP A4376 HIS 0.008 0.001 HIS A4466 Details of bonding type rmsd covalent geometry : bond 0.00341 (22340) covalent geometry : angle 0.67460 (30308) hydrogen bonds : bond 0.13977 ( 1251) hydrogen bonds : angle 5.98997 ( 3669) *********************** 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 : 0.593 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: 0.1515 time to fit residues: 60.7947 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 : 0.826 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN A2857 HIS A2998 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS A3988 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097655 restraints weight = 49601.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099378 restraints weight = 27445.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101144 restraints weight = 18816.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101247 restraints weight = 16635.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101312 restraints weight = 14542.956| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22340 Z= 0.179 Angle : 0.613 8.133 30308 Z= 0.308 Chirality : 0.041 0.163 3412 Planarity : 0.005 0.076 3883 Dihedral : 7.226 131.088 3026 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.83 % Allowed : 20.61 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.16), residues: 2699 helix: 1.74 (0.13), residues: 1524 sheet: -0.96 (0.35), residues: 201 loop : -0.06 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3007 TYR 0.024 0.002 TYR A2901 PHE 0.024 0.002 PHE A1727 TRP 0.018 0.001 TRP A2584 HIS 0.005 0.001 HIS A4100 Details of bonding type rmsd covalent geometry : bond 0.00413 (22340) covalent geometry : angle 0.61326 (30308) hydrogen bonds : bond 0.04526 ( 1251) hydrogen bonds : angle 4.87762 ( 3669) *********************** 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 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8684 (m-10) cc_final: 0.8410 (m-10) REVERT: A 1925 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7297 (mmt90) REVERT: A 1967 MET cc_start: 0.8540 (mtm) cc_final: 0.8236 (mtm) REVERT: A 2230 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: A 2231 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.5790 (p) REVERT: A 2670 ASP cc_start: 0.7066 (p0) cc_final: 0.6654 (p0) REVERT: A 2721 LYS cc_start: 0.8733 (mppt) cc_final: 0.8202 (mtmm) REVERT: A 2789 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7900 (mm-40) REVERT: A 2799 MET cc_start: 0.8058 (mmm) cc_final: 0.7619 (tpp) REVERT: A 2926 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: A 3113 MET cc_start: 0.6632 (mpp) cc_final: 0.5668 (tpt) REVERT: A 3684 PRO cc_start: 0.9133 (Cg_endo) cc_final: 0.8887 (Cg_exo) REVERT: A 3695 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.6671 (ttp-170) REVERT: A 4192 GLU cc_start: 0.7972 (mp0) cc_final: 0.7756 (mp0) outliers start: 68 outliers final: 39 residues processed: 303 average time/residue: 0.1443 time to fit residues: 69.1818 Evaluate side-chains 260 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 1923 LEU 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 2230 LYS 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 2448 ASP Chi-restraints excluded: chain A residue 2562 VAL 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 2926 PHE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3067 THR 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 38 optimal weight: 0.8980 chunk 214 optimal weight: 0.0980 chunk 216 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 252 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS ** A2689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS A3139 HIS A3499 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099608 restraints weight = 49540.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101710 restraints weight = 27763.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104158 restraints weight = 18556.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104338 restraints weight = 15615.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104154 restraints weight = 12925.340| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1176 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= 0.121 Angle : 0.562 10.025 30308 Z= 0.279 Chirality : 0.040 0.163 3412 Planarity : 0.004 0.056 3883 Dihedral : 6.841 126.778 3017 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.33 % Allowed : 21.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.16), residues: 2699 helix: 1.84 (0.13), residues: 1523 sheet: -0.87 (0.34), residues: 208 loop : 0.00 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3007 TYR 0.016 0.001 TYR A2901 PHE 0.028 0.001 PHE A1727 TRP 0.019 0.001 TRP A4376 HIS 0.004 0.001 HIS A2445 Details of bonding type rmsd covalent geometry : bond 0.00260 (22340) covalent geometry : angle 0.56176 (30308) hydrogen bonds : bond 0.04025 ( 1251) hydrogen bonds : angle 4.57674 ( 3669) *********************** 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 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8686 (m-10) cc_final: 0.8333 (m-10) REVERT: A 2012 MET cc_start: 0.8237 (tpp) cc_final: 0.7769 (tpp) REVERT: A 2231 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.5541 (p) REVERT: A 2721 LYS cc_start: 0.8782 (mppt) cc_final: 0.8304 (mtmm) REVERT: A 2755 MET cc_start: 0.6787 (tmm) cc_final: 0.6425 (tmm) REVERT: A 2799 MET cc_start: 0.7895 (mmm) cc_final: 0.7406 (tpp) REVERT: A 2926 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 3008 MET cc_start: 0.8448 (tpp) cc_final: 0.7525 (ttp) REVERT: A 3104 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7764 (mp10) REVERT: A 3113 MET cc_start: 0.6679 (mpp) cc_final: 0.5769 (tpt) REVERT: A 3684 PRO cc_start: 0.9108 (Cg_endo) cc_final: 0.8851 (Cg_exo) REVERT: A 3695 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.6600 (ttp-170) REVERT: A 3800 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7579 (mm-40) REVERT: A 4095 MET cc_start: 0.7359 (mmm) cc_final: 0.7034 (mmm) REVERT: A 4133 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (ttpp) REVERT: A 4192 GLU cc_start: 0.7999 (mp0) cc_final: 0.7716 (mp0) outliers start: 56 outliers final: 27 residues processed: 306 average time/residue: 0.1553 time to fit residues: 74.2366 Evaluate side-chains 255 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1923 LEU 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 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 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 3589 ILE Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4031 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 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4575 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 3 optimal weight: 0.0000 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2707 GLN ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.124542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099589 restraints weight = 49548.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101636 restraints weight = 27056.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103965 restraints weight = 17589.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104039 restraints weight = 14649.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104182 restraints weight = 12800.669| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1450 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= 0.122 Angle : 0.552 9.822 30308 Z= 0.275 Chirality : 0.040 0.159 3412 Planarity : 0.004 0.097 3883 Dihedral : 6.719 127.033 3016 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.70 % Allowed : 22.23 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.16), residues: 2699 helix: 1.87 (0.13), residues: 1529 sheet: -0.87 (0.34), residues: 215 loop : 0.02 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3088 TYR 0.014 0.001 TYR A2748 PHE 0.032 0.001 PHE A2682 TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2263 Details of bonding type rmsd covalent geometry : bond 0.00275 (22340) covalent geometry : angle 0.55195 (30308) hydrogen bonds : bond 0.03847 ( 1251) hydrogen bonds : angle 4.42193 ( 3669) *********************** 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 321 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8822 (mt) cc_final: 0.8611 (mt) REVERT: A 1889 TYR cc_start: 0.8665 (m-10) cc_final: 0.8309 (m-10) REVERT: A 2231 SER cc_start: 0.6934 (OUTLIER) cc_final: 0.5368 (p) REVERT: A 2422 ILE cc_start: 0.8347 (mm) cc_final: 0.8078 (mm) REVERT: A 2496 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 2510 MET cc_start: 0.7536 (ttt) cc_final: 0.6954 (ttt) REVERT: A 2513 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7961 (pt0) REVERT: A 2551 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7893 (mptt) REVERT: A 2670 ASP cc_start: 0.6892 (p0) cc_final: 0.6674 (p0) REVERT: A 2721 LYS cc_start: 0.8800 (mppt) cc_final: 0.8325 (mtmm) REVERT: A 2755 MET cc_start: 0.6580 (tmm) cc_final: 0.6205 (tmm) REVERT: A 2799 MET cc_start: 0.7879 (mmm) cc_final: 0.7415 (tpp) REVERT: A 2915 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 2926 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 3104 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: A 3113 MET cc_start: 0.6872 (mpp) cc_final: 0.5964 (tpt) REVERT: A 3620 ARG cc_start: 0.8694 (tpp80) cc_final: 0.8322 (mmm160) REVERT: A 3684 PRO cc_start: 0.9098 (Cg_endo) cc_final: 0.8831 (Cg_exo) REVERT: A 4095 MET cc_start: 0.7364 (mmm) cc_final: 0.7021 (mmm) REVERT: A 4133 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7639 (ttpp) REVERT: A 4192 GLU cc_start: 0.7963 (mp0) cc_final: 0.7688 (mp0) REVERT: A 4457 LYS cc_start: 0.8517 (tppt) cc_final: 0.7641 (mtmm) REVERT: A 4636 TYR cc_start: 0.8243 (m-80) cc_final: 0.7916 (m-80) outliers start: 65 outliers final: 38 residues processed: 311 average time/residue: 0.1573 time to fit residues: 76.6699 Evaluate side-chains 270 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1923 LEU 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 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL 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 2915 VAL 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 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 4002 LEU Chi-restraints excluded: chain A residue 4031 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 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4330 VAL 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 Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 250 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 265 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2689 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2954 ASN A2998 ASN A3200 HIS A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3845 r_free = 0.3845 target = 0.124341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099015 restraints weight = 49644.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.101354 restraints weight = 27957.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103299 restraints weight = 18054.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.103660 restraints weight = 14540.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103625 restraints weight = 13102.360| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.125 Angle : 0.559 9.001 30308 Z= 0.276 Chirality : 0.040 0.167 3412 Planarity : 0.004 0.046 3883 Dihedral : 6.833 163.395 3016 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.45 % Allowed : 22.85 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.16), residues: 2699 helix: 1.90 (0.13), residues: 1529 sheet: -0.93 (0.33), residues: 226 loop : 0.06 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3088 TYR 0.012 0.001 TYR A2748 PHE 0.033 0.001 PHE A1727 TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A2263 Details of bonding type rmsd covalent geometry : bond 0.00284 (22340) covalent geometry : angle 0.55941 (30308) hydrogen bonds : bond 0.03782 ( 1251) hydrogen bonds : angle 4.35345 ( 3669) *********************** 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 304 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8822 (mt) cc_final: 0.8607 (mt) REVERT: A 1889 TYR cc_start: 0.8699 (m-10) cc_final: 0.8340 (m-10) REVERT: A 1892 MET cc_start: 0.8511 (mmp) cc_final: 0.8277 (mmt) REVERT: A 2231 SER cc_start: 0.6561 (OUTLIER) cc_final: 0.6110 (m) REVERT: A 2279 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 2422 ILE cc_start: 0.8299 (mm) cc_final: 0.8022 (mm) REVERT: A 2496 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7528 (t80) REVERT: A 2510 MET cc_start: 0.7592 (ttm) cc_final: 0.7033 (ttt) REVERT: A 2551 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7948 (mptt) REVERT: A 2670 ASP cc_start: 0.6955 (p0) cc_final: 0.6453 (p0) REVERT: A 2721 LYS cc_start: 0.8876 (mppt) cc_final: 0.8527 (ptpp) REVERT: A 2755 MET cc_start: 0.6426 (tmm) cc_final: 0.6089 (tmm) REVERT: A 2799 MET cc_start: 0.7858 (mmm) cc_final: 0.7381 (tpp) REVERT: A 2915 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7706 (t) REVERT: A 3008 MET cc_start: 0.8127 (tpp) cc_final: 0.7234 (ttp) REVERT: A 3104 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: A 3113 MET cc_start: 0.6921 (mpp) cc_final: 0.5986 (tpt) REVERT: A 3620 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8256 (mmm160) REVERT: A 3684 PRO cc_start: 0.9094 (Cg_endo) cc_final: 0.8825 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7383 (mm-40) REVERT: A 4031 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 4192 GLU cc_start: 0.7968 (mp0) cc_final: 0.7616 (mp0) REVERT: A 4457 LYS cc_start: 0.8514 (tppt) cc_final: 0.7642 (mtmm) outliers start: 59 outliers final: 39 residues processed: 294 average time/residue: 0.1663 time to fit residues: 76.7368 Evaluate side-chains 271 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1923 LEU 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 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2279 LEU Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL 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 2915 VAL 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 3589 ILE Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4031 VAL 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 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4330 VAL 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 Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 0.0570 chunk 133 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2730 HIS A2886 GLN A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.123799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098234 restraints weight = 49280.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101061 restraints weight = 27247.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103746 restraints weight = 17045.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103643 restraints weight = 14691.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103688 restraints weight = 12560.190| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.131 Angle : 0.557 9.972 30308 Z= 0.275 Chirality : 0.040 0.160 3412 Planarity : 0.004 0.045 3883 Dihedral : 6.608 169.182 3014 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.07 % Allowed : 23.06 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.17), residues: 2699 helix: 1.93 (0.13), residues: 1527 sheet: -1.00 (0.33), residues: 235 loop : 0.11 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3088 TYR 0.012 0.001 TYR A2748 PHE 0.032 0.001 PHE A1727 TRP 0.018 0.001 TRP A2825 HIS 0.004 0.001 HIS A2263 Details of bonding type rmsd covalent geometry : bond 0.00300 (22340) covalent geometry : angle 0.55746 (30308) hydrogen bonds : bond 0.03742 ( 1251) hydrogen bonds : angle 4.29263 ( 3669) *********************** 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: 74 poor density : 242 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8855 (mt) cc_final: 0.8631 (mt) REVERT: A 1889 TYR cc_start: 0.8721 (m-10) cc_final: 0.8366 (m-10) REVERT: A 2210 LEU cc_start: 0.8431 (tp) cc_final: 0.8219 (tp) REVERT: A 2231 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.6467 (m) REVERT: A 2496 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7593 (t80) REVERT: A 2551 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7959 (mptt) REVERT: A 2670 ASP cc_start: 0.6895 (p0) cc_final: 0.6346 (p0) REVERT: A 2721 LYS cc_start: 0.8807 (mppt) cc_final: 0.8374 (ptpp) REVERT: A 2799 MET cc_start: 0.7868 (mmm) cc_final: 0.7410 (tpp) REVERT: A 2915 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7521 (t) REVERT: A 3008 MET cc_start: 0.8202 (tpp) cc_final: 0.7289 (ttp) REVERT: A 3104 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: A 3620 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8258 (mmm160) REVERT: A 3684 PRO cc_start: 0.9087 (Cg_endo) cc_final: 0.8812 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: A 4031 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8832 (p) REVERT: A 4171 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8430 (mmmm) REVERT: A 4192 GLU cc_start: 0.7971 (mp0) cc_final: 0.7079 (mp0) REVERT: A 4346 MET cc_start: 0.7482 (mmp) cc_final: 0.7093 (mmm) REVERT: A 4457 LYS cc_start: 0.8474 (tppt) cc_final: 0.7671 (ptpt) outliers start: 74 outliers final: 50 residues processed: 301 average time/residue: 0.1616 time to fit residues: 76.8997 Evaluate side-chains 278 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 1709 MET Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1923 LEU 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 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 2347 ASP Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR 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 2915 VAL Chi-restraints excluded: chain A residue 2933 LEU 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 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 4002 LEU Chi-restraints excluded: chain A residue 4031 VAL 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 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 4330 VAL 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 Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 247 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN A2263 HIS A2827 HIS ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094918 restraints weight = 50058.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096916 restraints weight = 28665.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098818 restraints weight = 19166.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099038 restraints weight = 17488.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098971 restraints weight = 14324.202| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22340 Z= 0.210 Angle : 0.639 10.386 30308 Z= 0.316 Chirality : 0.042 0.180 3412 Planarity : 0.005 0.085 3883 Dihedral : 6.242 122.917 3014 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.32 % Allowed : 23.35 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.16), residues: 2699 helix: 1.76 (0.13), residues: 1525 sheet: -1.03 (0.33), residues: 233 loop : 0.04 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1806 TYR 0.017 0.002 TYR A2496 PHE 0.031 0.002 PHE A1727 TRP 0.020 0.002 TRP A2825 HIS 0.006 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00487 (22340) covalent geometry : angle 0.63913 (30308) hydrogen bonds : bond 0.04255 ( 1251) hydrogen bonds : angle 4.44161 ( 3669) *********************** 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 308 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8893 (mt) cc_final: 0.8647 (mt) REVERT: A 1769 MET cc_start: 0.6625 (mmm) cc_final: 0.6244 (mmm) REVERT: A 1889 TYR cc_start: 0.8738 (m-10) cc_final: 0.8452 (m-10) REVERT: A 1892 MET cc_start: 0.8494 (mmp) cc_final: 0.8227 (mmt) REVERT: A 2231 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6402 (m) REVERT: A 2361 MET cc_start: 0.8436 (ttm) cc_final: 0.8029 (ttm) REVERT: A 2496 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 2551 LYS cc_start: 0.8326 (mmtp) cc_final: 0.8122 (mmtm) REVERT: A 2670 ASP cc_start: 0.6999 (p0) cc_final: 0.6428 (p0) REVERT: A 2721 LYS cc_start: 0.8837 (mppt) cc_final: 0.8398 (ptpp) REVERT: A 2755 MET cc_start: 0.6847 (tmm) cc_final: 0.6588 (tmm) REVERT: A 2799 MET cc_start: 0.8031 (mmm) cc_final: 0.7599 (tpp) REVERT: A 2825 TRP cc_start: 0.8610 (t60) cc_final: 0.8168 (t60) REVERT: A 3104 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: A 3620 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8309 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9089 (Cg_endo) cc_final: 0.8809 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7451 (mm-40) REVERT: A 4031 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 4171 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8551 (mmmm) REVERT: A 4192 GLU cc_start: 0.8025 (mp0) cc_final: 0.7202 (mp0) REVERT: A 4457 LYS cc_start: 0.8520 (tppt) cc_final: 0.7674 (ptpt) outliers start: 80 outliers final: 54 residues processed: 289 average time/residue: 0.1657 time to fit residues: 75.0735 Evaluate side-chains 273 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 1791 VAL Chi-restraints excluded: chain A residue 1923 LEU 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 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 2448 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR 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 2933 LEU 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 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4031 VAL 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 4330 VAL Chi-restraints excluded: chain A residue 4389 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 153 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2928 GLN A3200 HIS A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.124451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099767 restraints weight = 49311.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.102386 restraints weight = 25752.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.102793 restraints weight = 16689.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103608 restraints weight = 16357.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103535 restraints weight = 14505.808| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22340 Z= 0.120 Angle : 0.592 11.943 30308 Z= 0.290 Chirality : 0.040 0.192 3412 Planarity : 0.004 0.076 3883 Dihedral : 5.726 106.066 3014 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.49 % Allowed : 24.43 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.17), residues: 2699 helix: 1.86 (0.13), residues: 1524 sheet: -0.86 (0.35), residues: 206 loop : 0.08 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3088 TYR 0.012 0.001 TYR A2748 PHE 0.039 0.001 PHE A1727 TRP 0.021 0.001 TRP A2825 HIS 0.003 0.001 HIS A2263 Details of bonding type rmsd covalent geometry : bond 0.00268 (22340) covalent geometry : angle 0.59214 (30308) hydrogen bonds : bond 0.03773 ( 1251) hydrogen bonds : angle 4.26700 ( 3669) *********************** 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 294 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8838 (mt) cc_final: 0.8606 (mt) REVERT: A 1889 TYR cc_start: 0.8703 (m-10) cc_final: 0.8353 (m-10) REVERT: A 1892 MET cc_start: 0.8493 (mmp) cc_final: 0.8267 (mmt) REVERT: A 2012 MET cc_start: 0.8566 (tmm) cc_final: 0.8320 (tmm) REVERT: A 2231 SER cc_start: 0.6536 (OUTLIER) cc_final: 0.5910 (m) REVERT: A 2496 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 2670 ASP cc_start: 0.6994 (p0) cc_final: 0.6570 (p0) REVERT: A 2721 LYS cc_start: 0.8740 (mppt) cc_final: 0.8474 (mtmm) REVERT: A 2755 MET cc_start: 0.6909 (tmm) cc_final: 0.6538 (tmm) REVERT: A 2799 MET cc_start: 0.7866 (mmm) cc_final: 0.7425 (tpp) REVERT: A 2825 TRP cc_start: 0.8576 (t60) cc_final: 0.8029 (t60) REVERT: A 3008 MET cc_start: 0.8085 (tpp) cc_final: 0.7300 (ttp) REVERT: A 3104 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: A 3113 MET cc_start: 0.6723 (mpp) cc_final: 0.6518 (mpp) REVERT: A 3199 MET cc_start: 0.6834 (ptt) cc_final: 0.6517 (tmm) REVERT: A 3620 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8297 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9067 (Cg_endo) cc_final: 0.8789 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: A 4031 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 4171 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8451 (mmmm) REVERT: A 4192 GLU cc_start: 0.7998 (mp0) cc_final: 0.7099 (mp0) REVERT: A 4346 MET cc_start: 0.7579 (mmp) cc_final: 0.7250 (mmm) REVERT: A 4457 LYS cc_start: 0.8456 (tppt) cc_final: 0.7658 (ptpt) outliers start: 60 outliers final: 41 residues processed: 281 average time/residue: 0.1700 time to fit residues: 74.8603 Evaluate side-chains 268 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 1774 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE 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 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR 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 2953 MET Chi-restraints excluded: chain A residue 2961 ILE 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 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4031 VAL 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 4134 VAL 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 4389 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 260 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2857 HIS A2930 GLN A3852 HIS A4477 GLN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096176 restraints weight = 49786.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098845 restraints weight = 27354.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099832 restraints weight = 17812.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100159 restraints weight = 17161.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100056 restraints weight = 14032.210| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2343 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= 0.213 Angle : 0.646 10.694 30308 Z= 0.319 Chirality : 0.043 0.228 3412 Planarity : 0.004 0.072 3883 Dihedral : 5.650 106.729 3014 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.49 % Allowed : 24.47 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.16), residues: 2699 helix: 1.72 (0.13), residues: 1529 sheet: -0.95 (0.34), residues: 215 loop : -0.05 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2729 TYR 0.015 0.002 TYR A2496 PHE 0.034 0.002 PHE A1727 TRP 0.019 0.002 TRP A2825 HIS 0.005 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00495 (22340) covalent geometry : angle 0.64570 (30308) hydrogen bonds : bond 0.04136 ( 1251) hydrogen bonds : angle 4.40159 ( 3669) *********************** 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 281 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8882 (mt) cc_final: 0.8640 (mt) REVERT: A 1889 TYR cc_start: 0.8747 (m-10) cc_final: 0.8372 (m-10) REVERT: A 1892 MET cc_start: 0.8512 (mmp) cc_final: 0.8300 (mmt) REVERT: A 2012 MET cc_start: 0.8702 (tmm) cc_final: 0.8461 (tmm) REVERT: A 2231 SER cc_start: 0.7112 (OUTLIER) cc_final: 0.6533 (m) REVERT: A 2496 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7691 (t80) REVERT: A 2670 ASP cc_start: 0.7115 (p0) cc_final: 0.6690 (p0) REVERT: A 2721 LYS cc_start: 0.8768 (mppt) cc_final: 0.8462 (mtmm) REVERT: A 2755 MET cc_start: 0.6898 (tmm) cc_final: 0.6560 (tmm) REVERT: A 2789 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8439 (mm-40) REVERT: A 2799 MET cc_start: 0.7968 (mmm) cc_final: 0.7554 (tpp) REVERT: A 2825 TRP cc_start: 0.8599 (t60) cc_final: 0.8216 (t60) REVERT: A 3008 MET cc_start: 0.8063 (tpp) cc_final: 0.7191 (ttp) REVERT: A 3104 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 3620 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8231 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9088 (Cg_endo) cc_final: 0.8759 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7456 (mm-40) REVERT: A 4031 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8916 (p) REVERT: A 4171 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8539 (mmmm) REVERT: A 4192 GLU cc_start: 0.7943 (mp0) cc_final: 0.7091 (mp0) REVERT: A 4457 LYS cc_start: 0.8472 (tppt) cc_final: 0.7673 (ptpt) outliers start: 60 outliers final: 47 residues processed: 266 average time/residue: 0.1711 time to fit residues: 70.7060 Evaluate side-chains 266 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 1791 VAL Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE 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 2448 ASP 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 2583 THR 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 2679 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE 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 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4031 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 217 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 224 optimal weight: 0.0980 chunk 181 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 170 optimal weight: 0.0670 chunk 163 optimal weight: 9.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2857 HIS A3845 ASN A3852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102824 restraints weight = 50775.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106154 restraints weight = 25533.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108398 restraints weight = 16632.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109739 restraints weight = 12633.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110662 restraints weight = 10670.576| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22340 Z= 0.117 Angle : 0.599 11.763 30308 Z= 0.294 Chirality : 0.041 0.307 3412 Planarity : 0.004 0.069 3883 Dihedral : 5.475 107.567 3014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.99 % Allowed : 25.01 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.16), residues: 2699 helix: 1.84 (0.13), residues: 1524 sheet: -0.81 (0.35), residues: 206 loop : 0.05 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2060 TYR 0.015 0.001 TYR A2967 PHE 0.038 0.001 PHE A1727 TRP 0.022 0.001 TRP A2825 HIS 0.003 0.001 HIS A2263 Details of bonding type rmsd covalent geometry : bond 0.00261 (22340) covalent geometry : angle 0.59902 (30308) hydrogen bonds : bond 0.03719 ( 1251) hydrogen bonds : angle 4.25035 ( 3669) ********************** 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 289 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.879 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: 0.8798 (mt) cc_final: 0.8580 (mt) REVERT: A 1889 TYR cc_start: 0.8757 (m-10) cc_final: 0.8397 (m-10) REVERT: A 1892 MET cc_start: 0.8591 (mmp) cc_final: 0.8373 (mmt) REVERT: A 1925 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7550 (mmt90) REVERT: A 2231 SER cc_start: 0.6531 (OUTLIER) cc_final: 0.5972 (m) REVERT: A 2369 LEU cc_start: 0.8885 (mt) cc_final: 0.8430 (mt) REVERT: A 2496 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7619 (t80) REVERT: A 2721 LYS cc_start: 0.8726 (mppt) cc_final: 0.8513 (mtmm) REVERT: A 2755 MET cc_start: 0.7131 (tmm) cc_final: 0.6785 (tmm) REVERT: A 2799 MET cc_start: 0.7915 (mmm) cc_final: 0.7505 (tpp) REVERT: A 2825 TRP cc_start: 0.8564 (t60) cc_final: 0.8082 (t60) REVERT: A 2953 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6736 (tmm) REVERT: A 3008 MET cc_start: 0.7975 (tpp) cc_final: 0.7174 (ttp) REVERT: A 3104 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: A 3620 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8289 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9083 (Cg_endo) cc_final: 0.8780 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7439 (mm-40) REVERT: A 4031 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9024 (p) REVERT: A 4346 MET cc_start: 0.7644 (mmp) cc_final: 0.7341 (mmm) REVERT: A 4457 LYS cc_start: 0.8382 (tppt) cc_final: 0.7624 (ptpt) outliers start: 48 outliers final: 35 residues processed: 278 average time/residue: 0.1672 time to fit residues: 72.7782 Evaluate side-chains 261 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 1774 ASP Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE 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 2496 TYR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2603 MET 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 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4031 VAL 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 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.127959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100475 restraints weight = 51055.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103716 restraints weight = 26112.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105896 restraints weight = 17128.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107214 restraints weight = 13137.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107918 restraints weight = 11148.932| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22340 Z= 0.162 Angle : 0.620 11.808 30308 Z= 0.305 Chirality : 0.042 0.316 3412 Planarity : 0.004 0.068 3883 Dihedral : 5.505 108.791 3014 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.99 % Allowed : 25.30 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.16), residues: 2699 helix: 1.82 (0.13), residues: 1517 sheet: -0.91 (0.34), residues: 216 loop : -0.02 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3544 TYR 0.014 0.001 TYR A4636 PHE 0.038 0.002 PHE A1727 TRP 0.019 0.001 TRP A2825 HIS 0.004 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00378 (22340) covalent geometry : angle 0.61990 (30308) hydrogen bonds : bond 0.03866 ( 1251) hydrogen bonds : angle 4.28596 ( 3669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.15 seconds wall clock time: 63 minutes 19.28 seconds (3799.28 seconds total)