Starting phenix.real_space_refine on Thu May 22 02:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmo_44705/05_2025/9bmo_44705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmo_44705/05_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_44705/05_2025/9bmo_44705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmo_44705/05_2025/9bmo_44705.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmo_44705/05_2025/9bmo_44705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmo_44705/05_2025/9bmo_44705.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 111 5.16 5 C 13892 2.51 5 N 3777 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2711, 21755 Classifications: {'peptide': 2711} Link IDs: {'PTRANS': 126, 'TRANS': 2584} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.14, per 1000 atoms: 0.51 Number of scatterers: 21867 At special positions: 0 Unit cell: (148.428, 162.75, 121.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4078 8.00 N 3777 7.00 C 13892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 17 sheets defined 61.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.693A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.576A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1841 removed outlier: 4.204A pdb=" N GLN A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1924 Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.713A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.708A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2129 Processing helix chain 'A' and resid 2133 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.304A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.794A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.694A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.553A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.815A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.583A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.859A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.724A pdb=" N ARG A2576 " --> pdb=" O LEU A2572 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.543A pdb=" N ALA A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.941A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2731 removed outlier: 3.929A pdb=" N HIS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 4.235A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.869A pdb=" N LEU A2762 " --> pdb=" O ILE A2759 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.822A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.560A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.679A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3087 removed outlier: 3.508A pdb=" N PHE A3086 " --> pdb=" O PRO A3083 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.590A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 3.613A pdb=" N PHE A3496 " --> pdb=" O THR A3492 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 4.020A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.872A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3629 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3735 removed outlier: 3.783A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A3732 " --> pdb=" O ARG A3728 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A3733 " --> pdb=" O SER A3729 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3755 Processing helix chain 'A' and resid 3763 through 3793 removed outlier: 4.075A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3819 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.560A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3917 through 3921 Processing helix chain 'A' and resid 3928 through 3940 Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.949A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4019 removed outlier: 4.475A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.635A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.784A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.024A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.678A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.614A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.624A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.396A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.776A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.509A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4407 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 4.235A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.516A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 4.090A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.847A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A2017 " --> pdb=" O PHE A1957 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A1959 " --> pdb=" O THR A2017 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 8.012A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 removed outlier: 3.695A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2617 through 2620 removed outlier: 6.431A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A2734 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 3.658A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.265A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 3.523A pdb=" N LEU A3634 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.342A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.597A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A4589 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 3.624A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1251 hydrogen bonds defined for protein. 3669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 6.53 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 22340 Z= 0.146 Angle : 0.675 17.406 30308 Z= 0.349 Chirality : 0.041 0.230 3412 Planarity : 0.005 0.151 3883 Dihedral : 17.435 142.502 8390 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.46 % Allowed : 23.39 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2699 helix: 1.80 (0.13), residues: 1501 sheet: -0.92 (0.36), residues: 208 loop : -0.11 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A4376 HIS 0.008 0.001 HIS A4466 PHE 0.043 0.002 PHE A2972 TYR 0.041 0.002 TYR A4636 ARG 0.010 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.13977 ( 1251) hydrogen bonds : angle 5.98997 ( 3669) covalent geometry : bond 0.00341 (22340) covalent geometry : angle 0.67460 (30308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 2.592 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: 0.3375 time to fit residues: 136.0181 Evaluate side-chains 235 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS ** A2271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2730 HIS A2857 HIS A2998 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS A3906 GLN A3988 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095515 restraints weight = 49553.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097379 restraints weight = 27738.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099839 restraints weight = 19003.311| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22340 Z= 0.235 Angle : 0.662 8.487 30308 Z= 0.333 Chirality : 0.043 0.158 3412 Planarity : 0.005 0.077 3883 Dihedral : 7.372 135.777 3026 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.45 % Allowed : 20.57 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2699 helix: 1.62 (0.13), residues: 1524 sheet: -1.20 (0.32), residues: 235 loop : -0.02 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2584 HIS 0.006 0.001 HIS A3151 PHE 0.024 0.002 PHE A1727 TYR 0.023 0.002 TYR A2901 ARG 0.005 0.001 ARG A4176 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1251) hydrogen bonds : angle 4.92535 ( 3669) covalent geometry : bond 0.00545 (22340) covalent geometry : angle 0.66156 (30308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 245 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8751 (m-10) cc_final: 0.8469 (m-10) REVERT: A 2012 MET cc_start: 0.8413 (tpp) cc_final: 0.7949 (tpp) REVERT: A 2231 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.5701 (p) REVERT: A 2582 TYR cc_start: 0.8009 (t80) cc_final: 0.7733 (t80) REVERT: A 2585 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 2670 ASP cc_start: 0.7028 (p0) cc_final: 0.6615 (p0) REVERT: A 2721 LYS cc_start: 0.8731 (mppt) cc_final: 0.8172 (mtmm) REVERT: A 2799 MET cc_start: 0.8137 (mmm) cc_final: 0.7714 (tpp) REVERT: A 2926 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: A 3104 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 3113 MET cc_start: 0.6719 (mpp) cc_final: 0.5778 (tpt) REVERT: A 3684 PRO cc_start: 0.9134 (Cg_endo) cc_final: 0.8877 (Cg_exo) REVERT: A 4192 GLU cc_start: 0.8007 (mp0) cc_final: 0.7720 (mp0) outliers start: 83 outliers final: 46 residues processed: 313 average time/residue: 0.3404 time to fit residues: 168.1138 Evaluate side-chains 266 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2412 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2903 GLU Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2947 SER Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4389 HIS Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 139 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2857 HIS A3139 HIS ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3538 GLN A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098202 restraints weight = 48893.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100532 restraints weight = 26644.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102754 restraints weight = 17369.293| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1272 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= 0.126 Angle : 0.573 8.991 30308 Z= 0.283 Chirality : 0.040 0.163 3412 Planarity : 0.004 0.059 3883 Dihedral : 6.964 132.059 3017 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.29 % Allowed : 22.39 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2699 helix: 1.76 (0.13), residues: 1529 sheet: -0.93 (0.34), residues: 207 loop : -0.02 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4376 HIS 0.003 0.001 HIS A2263 PHE 0.028 0.001 PHE A1727 TYR 0.017 0.001 TYR A4636 ARG 0.004 0.000 ARG A3007 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1251) hydrogen bonds : angle 4.61250 ( 3669) covalent geometry : bond 0.00281 (22340) covalent geometry : angle 0.57277 (30308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1889 TYR cc_start: 0.8663 (m-10) cc_final: 0.8406 (m-10) REVERT: A 2012 MET cc_start: 0.8450 (tpp) cc_final: 0.7981 (tpp) REVERT: A 2231 SER cc_start: 0.7166 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 2551 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7979 (mptt) REVERT: A 2582 TYR cc_start: 0.7905 (t80) cc_final: 0.7656 (t80) REVERT: A 2670 ASP cc_start: 0.6965 (p0) cc_final: 0.6553 (p0) REVERT: A 2688 GLU cc_start: 0.7926 (tt0) cc_final: 0.7682 (tt0) REVERT: A 2721 LYS cc_start: 0.8783 (mppt) cc_final: 0.8311 (mtmm) REVERT: A 2755 MET cc_start: 0.6746 (tmm) cc_final: 0.6455 (tmm) REVERT: A 2799 MET cc_start: 0.7943 (mmm) cc_final: 0.7480 (tpp) REVERT: A 3008 MET cc_start: 0.8437 (tpp) cc_final: 0.7496 (ttp) REVERT: A 3104 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: A 3113 MET cc_start: 0.6733 (mpp) cc_final: 0.5831 (tpt) REVERT: A 3684 PRO cc_start: 0.9107 (Cg_endo) cc_final: 0.8852 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7495 (tp40) REVERT: A 4095 MET cc_start: 0.7516 (mmm) cc_final: 0.7206 (mmm) REVERT: A 4133 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7613 (ttpp) REVERT: A 4192 GLU cc_start: 0.8039 (mp0) cc_final: 0.7759 (mp0) outliers start: 55 outliers final: 30 residues processed: 295 average time/residue: 0.3419 time to fit residues: 158.2761 Evaluate side-chains 252 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 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 2448 ASP Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 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 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 260 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2707 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095960 restraints weight = 50285.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097920 restraints weight = 27639.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099631 restraints weight = 18096.755| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22340 Z= 0.178 Angle : 0.597 10.548 30308 Z= 0.297 Chirality : 0.041 0.164 3412 Planarity : 0.005 0.090 3883 Dihedral : 7.012 137.452 3016 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.49 % Allowed : 22.35 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.16), residues: 2699 helix: 1.74 (0.13), residues: 1525 sheet: -0.95 (0.35), residues: 203 loop : -0.02 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.004 0.001 HIS A2588 PHE 0.029 0.002 PHE A1727 TYR 0.020 0.002 TYR A3516 ARG 0.017 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1251) hydrogen bonds : angle 4.54010 ( 3669) covalent geometry : bond 0.00412 (22340) covalent geometry : angle 0.59721 (30308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 248 time to evaluate : 2.567 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: 0.8853 (mt) cc_final: 0.8641 (mt) REVERT: A 1889 TYR cc_start: 0.8732 (m-10) cc_final: 0.8511 (m-10) REVERT: A 2231 SER cc_start: 0.6973 (OUTLIER) cc_final: 0.5355 (p) REVERT: A 2496 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7497 (t80) REVERT: A 2510 MET cc_start: 0.7607 (ttt) cc_final: 0.7195 (ttt) REVERT: A 2551 LYS cc_start: 0.8292 (mmtp) cc_final: 0.8035 (mptt) REVERT: A 2670 ASP cc_start: 0.7044 (p0) cc_final: 0.6609 (p0) REVERT: A 2721 LYS cc_start: 0.8840 (mppt) cc_final: 0.8372 (mtmm) REVERT: A 2755 MET cc_start: 0.6536 (tmm) cc_final: 0.6184 (tmm) REVERT: A 2799 MET cc_start: 0.7987 (mmm) cc_final: 0.7569 (tpp) REVERT: A 2966 LYS cc_start: 0.8686 (tptt) cc_final: 0.8322 (mmtt) REVERT: A 3104 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: A 3113 MET cc_start: 0.7037 (mpp) cc_final: 0.6107 (tpt) REVERT: A 3684 PRO cc_start: 0.9110 (Cg_endo) cc_final: 0.8848 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7519 (tp40) REVERT: A 4095 MET cc_start: 0.7688 (mmm) cc_final: 0.7338 (mmm) REVERT: A 4133 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7682 (ttpp) REVERT: A 4192 GLU cc_start: 0.8029 (mp0) cc_final: 0.7685 (mp0) REVERT: A 4457 LYS cc_start: 0.8502 (tppt) cc_final: 0.7631 (mtmm) outliers start: 84 outliers final: 53 residues processed: 316 average time/residue: 0.3458 time to fit residues: 171.0496 Evaluate side-chains 276 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2356 VAL 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 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 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 3703 VAL Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4521 ILE Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2707 GLN A3555 ASN 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 = 0.3830 r_free = 0.3830 target = 0.123191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098223 restraints weight = 49515.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100400 restraints weight = 27085.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102660 restraints weight = 17530.317| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1741 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 : 0.566 9.711 30308 Z= 0.279 Chirality : 0.040 0.159 3412 Planarity : 0.004 0.074 3883 Dihedral : 6.825 127.235 3016 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 23.14 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2699 helix: 1.83 (0.13), residues: 1525 sheet: -1.07 (0.34), residues: 217 loop : 0.05 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A2560 PHE 0.028 0.001 PHE A1727 TYR 0.014 0.001 TYR A3516 ARG 0.008 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1251) hydrogen bonds : angle 4.39059 ( 3669) covalent geometry : bond 0.00269 (22340) covalent geometry : angle 0.56571 (30308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 2.414 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: 0.8820 (mt) cc_final: 0.8593 (mt) REVERT: A 1889 TYR cc_start: 0.8672 (m-10) cc_final: 0.8393 (m-10) REVERT: A 2012 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7131 (tpp) REVERT: A 2231 SER cc_start: 0.6646 (OUTLIER) cc_final: 0.6208 (m) REVERT: A 2422 ILE cc_start: 0.8226 (mm) cc_final: 0.7960 (mm) REVERT: A 2496 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 2510 MET cc_start: 0.7713 (ttt) cc_final: 0.7491 (ttt) REVERT: A 2551 LYS cc_start: 0.8273 (mmtp) cc_final: 0.8016 (mptt) REVERT: A 2585 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 2721 LYS cc_start: 0.8902 (mppt) cc_final: 0.8590 (ptpp) REVERT: A 2799 MET cc_start: 0.7872 (mmm) cc_final: 0.7442 (tpp) REVERT: A 2966 LYS cc_start: 0.8687 (tptt) cc_final: 0.8344 (mmtt) REVERT: A 3008 MET cc_start: 0.8085 (tpp) cc_final: 0.7226 (ttp) REVERT: A 3104 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: A 3620 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8235 (mmm160) REVERT: A 3684 PRO cc_start: 0.9086 (Cg_endo) cc_final: 0.8813 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7466 (tp40) REVERT: A 4133 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7640 (ttpp) REVERT: A 4192 GLU cc_start: 0.8042 (mp0) cc_final: 0.7719 (mp0) outliers start: 65 outliers final: 38 residues processed: 310 average time/residue: 0.3264 time to fit residues: 159.3326 Evaluate side-chains 272 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 1766 LEU Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 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 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4575 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 6 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2827 HIS ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3803 r_free = 0.3803 target = 0.121374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096078 restraints weight = 49654.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098254 restraints weight = 27851.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100194 restraints weight = 18037.512| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22340 Z= 0.161 Angle : 0.583 8.360 30308 Z= 0.290 Chirality : 0.041 0.207 3412 Planarity : 0.004 0.063 3883 Dihedral : 6.622 129.865 3014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.45 % Allowed : 23.06 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2699 helix: 1.74 (0.13), residues: 1535 sheet: -1.08 (0.34), residues: 224 loop : 0.00 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2825 HIS 0.005 0.001 HIS A2560 PHE 0.031 0.002 PHE A1727 TYR 0.016 0.001 TYR A3516 ARG 0.005 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 1251) hydrogen bonds : angle 4.37703 ( 3669) covalent geometry : bond 0.00372 (22340) covalent geometry : angle 0.58308 (30308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 235 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8834 (mt) cc_final: 0.8610 (mt) REVERT: A 1889 TYR cc_start: 0.8709 (m-10) cc_final: 0.8482 (m-10) REVERT: A 1974 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (mm110) REVERT: A 2231 SER cc_start: 0.6802 (OUTLIER) cc_final: 0.6394 (m) REVERT: A 2361 MET cc_start: 0.8550 (ttm) cc_final: 0.8153 (ttm) REVERT: A 2496 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 2510 MET cc_start: 0.7795 (ttm) cc_final: 0.7506 (ttt) REVERT: A 2670 ASP cc_start: 0.6959 (p0) cc_final: 0.6526 (p0) REVERT: A 2755 MET cc_start: 0.6937 (tmm) cc_final: 0.6571 (tmm) REVERT: A 2799 MET cc_start: 0.7961 (mmm) cc_final: 0.7547 (tpp) REVERT: A 2825 TRP cc_start: 0.8546 (t60) cc_final: 0.8057 (t60) REVERT: A 3008 MET cc_start: 0.8203 (tpp) cc_final: 0.7247 (ttp) REVERT: A 3104 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: A 3113 MET cc_start: 0.6772 (mpp) cc_final: 0.5566 (tpt) REVERT: A 3620 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8267 (mmm160) REVERT: A 3684 PRO cc_start: 0.9078 (Cg_endo) cc_final: 0.8797 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7488 (tp40) REVERT: A 4133 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7650 (ttpp) REVERT: A 4171 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8497 (mmmm) REVERT: A 4192 GLU cc_start: 0.8031 (mp0) cc_final: 0.7155 (mp0) outliers start: 83 outliers final: 57 residues processed: 301 average time/residue: 0.3536 time to fit residues: 166.6752 Evaluate side-chains 281 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 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 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 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 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain A residue 4626 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2485 GLN A2857 HIS A3852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.095167 restraints weight = 49965.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097800 restraints weight = 28443.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099354 restraints weight = 18021.767| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22340 Z= 0.174 Angle : 0.596 11.233 30308 Z= 0.295 Chirality : 0.041 0.175 3412 Planarity : 0.004 0.058 3883 Dihedral : 6.455 136.921 3014 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.61 % Allowed : 23.10 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2699 helix: 1.74 (0.13), residues: 1529 sheet: -1.01 (0.34), residues: 225 loop : -0.01 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2825 HIS 0.005 0.001 HIS A4100 PHE 0.031 0.002 PHE A1727 TYR 0.015 0.001 TYR A3516 ARG 0.008 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 1251) hydrogen bonds : angle 4.36671 ( 3669) covalent geometry : bond 0.00403 (22340) covalent geometry : angle 0.59567 (30308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 226 time to evaluate : 2.324 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: 0.8830 (mt) cc_final: 0.8600 (mt) REVERT: A 1889 TYR cc_start: 0.8761 (m-10) cc_final: 0.8505 (m-10) REVERT: A 2012 MET cc_start: 0.8633 (tmm) cc_final: 0.8362 (tmm) REVERT: A 2231 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6183 (m) REVERT: A 2496 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 2510 MET cc_start: 0.7887 (ttm) cc_final: 0.7416 (ttt) REVERT: A 2671 MET cc_start: 0.7684 (mmm) cc_final: 0.7315 (mmm) REVERT: A 2755 MET cc_start: 0.7092 (tmm) cc_final: 0.6788 (tmm) REVERT: A 2799 MET cc_start: 0.7987 (mmm) cc_final: 0.7577 (tpp) REVERT: A 2825 TRP cc_start: 0.8586 (t60) cc_final: 0.8174 (t60) REVERT: A 2966 LYS cc_start: 0.8678 (tptt) cc_final: 0.8368 (mmtt) REVERT: A 3104 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: A 3113 MET cc_start: 0.6831 (mpp) cc_final: 0.6604 (mpp) REVERT: A 3620 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8322 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9079 (Cg_endo) cc_final: 0.8800 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: A 4171 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (mmmm) REVERT: A 4192 GLU cc_start: 0.8041 (mp0) cc_final: 0.7135 (mp0) REVERT: A 4457 LYS cc_start: 0.8559 (tppt) cc_final: 0.7691 (ptpt) outliers start: 87 outliers final: 64 residues processed: 295 average time/residue: 0.3252 time to fit residues: 150.9445 Evaluate side-chains 285 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3067 THR Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3856 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 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 131 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2263 HIS ** A2886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN A3852 HIS A4477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098734 restraints weight = 49532.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101211 restraints weight = 27963.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102860 restraints weight = 17427.257| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2234 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= 0.119 Angle : 0.569 12.180 30308 Z= 0.279 Chirality : 0.040 0.217 3412 Planarity : 0.004 0.054 3883 Dihedral : 6.208 138.539 3014 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.20 % Allowed : 24.51 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.16), residues: 2699 helix: 1.84 (0.13), residues: 1529 sheet: -0.94 (0.34), residues: 216 loop : 0.01 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2825 HIS 0.004 0.001 HIS A2560 PHE 0.035 0.001 PHE A1727 TYR 0.011 0.001 TYR A2748 ARG 0.006 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1251) hydrogen bonds : angle 4.24115 ( 3669) covalent geometry : bond 0.00267 (22340) covalent geometry : angle 0.56873 (30308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8831 (mt) cc_final: 0.8595 (mt) REVERT: A 1889 TYR cc_start: 0.8703 (m-10) cc_final: 0.8493 (m-10) REVERT: A 2012 MET cc_start: 0.8569 (tmm) cc_final: 0.8341 (tmm) REVERT: A 2231 SER cc_start: 0.6546 (OUTLIER) cc_final: 0.5941 (m) REVERT: A 2369 LEU cc_start: 0.8902 (mt) cc_final: 0.8346 (mt) REVERT: A 2496 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 2510 MET cc_start: 0.7947 (ttm) cc_final: 0.7581 (ttt) REVERT: A 2610 ARG cc_start: 0.7415 (ppt170) cc_final: 0.7120 (ppt170) REVERT: A 2671 MET cc_start: 0.7602 (mmm) cc_final: 0.7268 (mmm) REVERT: A 2755 MET cc_start: 0.7140 (tmm) cc_final: 0.6824 (tmm) REVERT: A 2799 MET cc_start: 0.7877 (mmm) cc_final: 0.7475 (tpp) REVERT: A 2825 TRP cc_start: 0.8567 (t60) cc_final: 0.8041 (t60) REVERT: A 3008 MET cc_start: 0.8081 (tpp) cc_final: 0.7285 (ttp) REVERT: A 3113 MET cc_start: 0.6723 (mpp) cc_final: 0.6514 (mpp) REVERT: A 3620 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8309 (tpp-160) REVERT: A 3684 PRO cc_start: 0.9076 (Cg_endo) cc_final: 0.8797 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: A 4192 GLU cc_start: 0.8000 (mp0) cc_final: 0.7048 (mp0) REVERT: A 4457 LYS cc_start: 0.8508 (tppt) cc_final: 0.7659 (ptpt) outliers start: 53 outliers final: 40 residues processed: 279 average time/residue: 0.3407 time to fit residues: 149.3711 Evaluate side-chains 264 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 1766 LEU Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1960 PHE 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 2276 THR Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 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 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 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU 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 4575 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.0000 chunk 131 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2857 HIS A2886 GLN A2913 ASN A2930 GLN A3852 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102651 restraints weight = 50846.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105933 restraints weight = 25551.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108176 restraints weight = 16654.761| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2318 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= 0.119 Angle : 0.581 11.083 30308 Z= 0.284 Chirality : 0.040 0.292 3412 Planarity : 0.004 0.052 3883 Dihedral : 6.141 139.860 3014 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.37 % Allowed : 24.76 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.16), residues: 2699 helix: 1.88 (0.13), residues: 1529 sheet: -0.78 (0.35), residues: 206 loop : 0.03 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A2560 PHE 0.038 0.001 PHE A1727 TYR 0.017 0.001 TYR A2967 ARG 0.006 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1251) hydrogen bonds : angle 4.20738 ( 3669) covalent geometry : bond 0.00266 (22340) covalent geometry : angle 0.58066 (30308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 LEU cc_start: 0.8831 (mt) cc_final: 0.8593 (mt) REVERT: A 1889 TYR cc_start: 0.8809 (m-10) cc_final: 0.8596 (m-10) REVERT: A 1925 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7584 (mmt90) REVERT: A 2012 MET cc_start: 0.8670 (tmm) cc_final: 0.8462 (tmm) REVERT: A 2231 SER cc_start: 0.6625 (OUTLIER) cc_final: 0.6005 (m) REVERT: A 2369 LEU cc_start: 0.8780 (mt) cc_final: 0.8227 (mt) REVERT: A 2496 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7540 (t80) REVERT: A 2510 MET cc_start: 0.8004 (ttm) cc_final: 0.7609 (ttt) REVERT: A 2610 ARG cc_start: 0.7410 (ppt170) cc_final: 0.7084 (ppt170) REVERT: A 2671 MET cc_start: 0.7580 (mmm) cc_final: 0.7224 (mmm) REVERT: A 2755 MET cc_start: 0.7184 (tmm) cc_final: 0.6876 (tmm) REVERT: A 2799 MET cc_start: 0.7922 (mmm) cc_final: 0.7521 (tpp) REVERT: A 2825 TRP cc_start: 0.8635 (t60) cc_final: 0.8131 (t60) REVERT: A 2886 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: A 2953 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6900 (tmm) REVERT: A 3008 MET cc_start: 0.8080 (tpp) cc_final: 0.7216 (ttp) REVERT: A 3104 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7669 (mp10) REVERT: A 3620 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8319 (mmm160) REVERT: A 3684 PRO cc_start: 0.9085 (Cg_endo) cc_final: 0.8788 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7217 (mm-40) REVERT: A 4192 GLU cc_start: 0.7943 (mp0) cc_final: 0.7085 (mp0) REVERT: A 4346 MET cc_start: 0.7621 (mmp) cc_final: 0.7312 (mmm) REVERT: A 4457 LYS cc_start: 0.8507 (tppt) cc_final: 0.7655 (ptpt) outliers start: 57 outliers final: 42 residues processed: 278 average time/residue: 0.3436 time to fit residues: 150.8222 Evaluate side-chains 270 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1912 LYS 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 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2886 GLN 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 3809 SER Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 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 4575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 chunk 231 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 176 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2263 HIS A2886 GLN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102182 restraints weight = 50817.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105472 restraints weight = 25599.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107680 restraints weight = 16671.910| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2408 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= 0.124 Angle : 0.590 11.653 30308 Z= 0.289 Chirality : 0.041 0.300 3412 Planarity : 0.004 0.052 3883 Dihedral : 6.126 141.393 3014 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.29 % Allowed : 25.14 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 2699 helix: 1.89 (0.13), residues: 1530 sheet: -0.82 (0.35), residues: 206 loop : 0.02 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A2918 PHE 0.039 0.001 PHE A1727 TYR 0.022 0.001 TYR A3516 ARG 0.006 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1251) hydrogen bonds : angle 4.19386 ( 3669) covalent geometry : bond 0.00280 (22340) covalent geometry : angle 0.58973 (30308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 2.378 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: 0.8827 (mt) cc_final: 0.8594 (mt) REVERT: A 1889 TYR cc_start: 0.8788 (m-10) cc_final: 0.8561 (m-10) REVERT: A 1925 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7561 (mmt90) REVERT: A 2231 SER cc_start: 0.6795 (OUTLIER) cc_final: 0.6137 (m) REVERT: A 2369 LEU cc_start: 0.8869 (mt) cc_final: 0.8271 (mt) REVERT: A 2496 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7549 (t80) REVERT: A 2510 MET cc_start: 0.7978 (ttm) cc_final: 0.7595 (ttt) REVERT: A 2610 ARG cc_start: 0.7410 (ppt170) cc_final: 0.7121 (ppt170) REVERT: A 2671 MET cc_start: 0.7586 (mmm) cc_final: 0.7232 (mmm) REVERT: A 2755 MET cc_start: 0.7185 (tmm) cc_final: 0.6883 (tmm) REVERT: A 2799 MET cc_start: 0.7888 (mmm) cc_final: 0.7487 (tpp) REVERT: A 2825 TRP cc_start: 0.8590 (t60) cc_final: 0.8110 (t60) REVERT: A 2953 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6890 (tmm) REVERT: A 3008 MET cc_start: 0.8085 (tpp) cc_final: 0.7196 (ttp) REVERT: A 3104 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: A 3620 ARG cc_start: 0.8648 (tpp80) cc_final: 0.8317 (mmm160) REVERT: A 3684 PRO cc_start: 0.9100 (Cg_endo) cc_final: 0.8803 (Cg_exo) REVERT: A 3800 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7146 (mm-40) REVERT: A 4192 GLU cc_start: 0.7928 (mp0) cc_final: 0.7046 (mp0) REVERT: A 4346 MET cc_start: 0.7688 (mmp) cc_final: 0.7401 (mmm) REVERT: A 4457 LYS cc_start: 0.8494 (tppt) cc_final: 0.7670 (ptpt) outliers start: 55 outliers final: 44 residues processed: 271 average time/residue: 0.3394 time to fit residues: 145.8130 Evaluate side-chains 274 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1774 ASP Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1912 LYS 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 2150 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR 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 2580 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2679 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 3676 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3800 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 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 4575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 252 optimal weight: 0.0170 chunk 155 optimal weight: 6.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1841 GLN A2263 HIS A2849 ASN A2857 HIS A2886 GLN A2998 ASN ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4100 HIS ** 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 = 0.4012 r_free = 0.4012 target = 0.129934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.102928 restraints weight = 50808.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106238 restraints weight = 25627.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108325 restraints weight = 16694.081| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2479 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= 0.118 Angle : 0.585 11.885 30308 Z= 0.286 Chirality : 0.040 0.291 3412 Planarity : 0.004 0.051 3883 Dihedral : 6.095 143.861 3014 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.20 % Allowed : 25.01 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.16), residues: 2699 helix: 1.93 (0.13), residues: 1523 sheet: -0.77 (0.34), residues: 214 loop : 0.03 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2825 HIS 0.004 0.001 HIS A2560 PHE 0.039 0.001 PHE A1727 TYR 0.020 0.001 TYR A3516 ARG 0.009 0.000 ARG A1623 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1251) hydrogen bonds : angle 4.15380 ( 3669) covalent geometry : bond 0.00265 (22340) covalent geometry : angle 0.58490 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6502.98 seconds wall clock time: 115 minutes 9.64 seconds (6909.64 seconds total)