Starting phenix.real_space_refine on Fri Sep 19 02:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm7_44690/09_2025/9bm7_44690.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 10 5.49 5 S 110 5.16 5 C 13868 2.51 5 N 3768 2.21 5 O 4062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21818 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2703, 21702 Classifications: {'peptide': 2703} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 126, 'TRANS': 2576} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.77, per 1000 atoms: 0.22 Number of scatterers: 21818 At special positions: 0 Unit cell: (149.76, 151.424, 123.968, 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 110 16.00 P 10 15.00 O 4062 8.00 N 3768 7.00 C 13868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 887.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 18 sheets defined 60.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 1615 through 1626 Processing helix chain 'A' and resid 1627 through 1631 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1650 removed outlier: 4.038A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 4.322A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A1658 " --> pdb=" O PHE A1654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1653 through 1658' Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.528A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1768 Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.856A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1824 removed outlier: 3.541A pdb=" N SER A1824 " --> pdb=" O ASP A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1912 through 1924 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.505A pdb=" N ARG A1962 " --> pdb=" O GLU A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1985 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.620A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 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 2150 through 2151 No H-bonds generated for 'chain 'A' and resid 2150 through 2151' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.222A 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 2230 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.535A pdb=" N VAL A2356 " --> pdb=" O THR A2352 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.609A 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 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.569A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2502 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 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.808A pdb=" N ALA A2579 " --> pdb=" O VAL A2575 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.789A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.231A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.037A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2783 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.899A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2835 through 2837 No H-bonds generated for 'chain 'A' and resid 2835 through 2837' Processing helix chain 'A' and resid 2839 through 2858 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: 3.847A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3083 through 3087 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: 3.589A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3502 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.781A pdb=" N TYR A3552 " --> pdb=" O ALA A3548 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3548 through 3553' 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 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.510A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) 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 removed outlier: 3.716A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3735 removed outlier: 4.143A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 Processing helix chain 'A' and resid 3762 through 3786 Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.191A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.214A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.506A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4032 removed outlier: 4.224A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.879A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4091 removed outlier: 3.996A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4114 removed outlier: 3.759A pdb=" N HIS A4114 " --> pdb=" O GLU A4110 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.638A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.031A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4197 through 4202 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.646A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4251 through 4255 removed outlier: 3.995A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) 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: 3.726A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4325 through 4346 removed outlier: 4.441A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 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 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.109A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4531 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 10.618A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.843A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.198A 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 1901 through 1903 removed outlier: 6.536A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.265A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 3.594A pdb=" N PHE A2343 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 3.527A pdb=" N ALA A2711 " --> pdb=" O CYS A2663 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2642 Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.447A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.480A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3661 through 3664 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 5.540A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.830A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4508 through 4510 Processing sheet with id=AB9, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.728A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7042 1.34 - 1.46: 3915 1.46 - 1.58: 11139 1.58 - 1.70: 13 1.70 - 1.82: 183 Bond restraints: 22292 Sorted by residual: bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" N VAL A1880 " pdb=" CA VAL A1880 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ILE A2049 " pdb=" CA ILE A2049 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.14e-02 7.69e+03 7.73e+00 bond pdb=" N LEU A1879 " pdb=" CA LEU A1879 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.22e-02 6.72e+03 6.76e+00 ... (remaining 22287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 29796 2.41 - 4.81: 358 4.81 - 7.22: 72 7.22 - 9.63: 17 9.63 - 12.03: 5 Bond angle restraints: 30248 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 130.98 8.89 1.00e+00 1.00e+00 7.91e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 131.77 5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 98.97 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CB MET A4021 " pdb=" CG MET A4021 " pdb=" SD MET A4021 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA MET A2221 " pdb=" CB MET A2221 " pdb=" CG MET A2221 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 ... (remaining 30243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11479 17.90 - 35.80: 1530 35.80 - 53.70: 405 53.70 - 71.60: 90 71.60 - 89.50: 23 Dihedral angle restraints: 13527 sinusoidal: 5616 harmonic: 7911 Sorted by residual: dihedral pdb=" CA GLY A2360 " pdb=" C GLY A2360 " pdb=" N MET A2361 " pdb=" CA MET A2361 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA CYS A2359 " pdb=" C CYS A2359 " pdb=" N GLY A2360 " pdb=" CA GLY A2360 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TYR A3125 " pdb=" C TYR A3125 " pdb=" N MET A3126 " pdb=" CA MET A3126 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 13524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2706 0.049 - 0.098: 556 0.098 - 0.147: 124 0.147 - 0.196: 16 0.196 - 0.245: 4 Chirality restraints: 3406 Sorted by residual: chirality pdb=" CB ILE A3835 " pdb=" CA ILE A3835 " pdb=" CG1 ILE A3835 " pdb=" CG2 ILE A3835 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE A2049 " pdb=" N ILE A2049 " pdb=" C ILE A2049 " pdb=" CB ILE A2049 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PHE A2926 " pdb=" N PHE A2926 " pdb=" C PHE A2926 " pdb=" CB PHE A2926 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3403 not shown) Planarity restraints: 3871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3683 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO A3684 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO A3684 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A3684 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A4105 " 0.027 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP A4105 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A4105 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A4105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A4105 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A4105 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A4105 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4105 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A4105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A2811 " 0.061 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO A2812 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A2812 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2812 " 0.050 5.00e-02 4.00e+02 ... (remaining 3868 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 489 2.68 - 3.23: 22687 3.23 - 3.79: 36871 3.79 - 4.34: 46155 4.34 - 4.90: 75162 Nonbonded interactions: 181364 Sorted by model distance: nonbonded pdb=" OH TYR A2426 " pdb=" OE1 GLN A2491 " model vdw 2.125 3.040 nonbonded pdb=" OD1 ASP A2995 " pdb=" OG1 THR A3067 " model vdw 2.150 3.040 nonbonded pdb=" OG SER A2983 " pdb=" O ASN A3061 " model vdw 2.153 3.040 nonbonded pdb=" OG SER A2542 " pdb=" OE1 GLU A2544 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.192 3.040 ... (remaining 181359 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: 4.620 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 22292 Z= 0.209 Angle : 0.691 12.032 30248 Z= 0.359 Chirality : 0.043 0.245 3406 Planarity : 0.005 0.123 3871 Dihedral : 17.578 89.503 8387 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 0.58 % Allowed : 26.66 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.16), residues: 2689 helix: 2.14 (0.13), residues: 1440 sheet: -0.32 (0.34), residues: 225 loop : -0.00 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A2831 TYR 0.023 0.001 TYR A3176 PHE 0.023 0.001 PHE A2635 TRP 0.064 0.002 TRP A4105 HIS 0.019 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00437 (22292) covalent geometry : angle 0.69101 (30248) hydrogen bonds : bond 0.13377 ( 1244) hydrogen bonds : angle 5.84688 ( 3618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1880 VAL cc_start: 0.8968 (t) cc_final: 0.8755 (t) REVERT: A 2342 MET cc_start: 0.8199 (mmm) cc_final: 0.7475 (mmt) outliers start: 14 outliers final: 5 residues processed: 250 average time/residue: 0.1351 time to fit residues: 56.6812 Evaluate side-chains 237 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 232 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2780 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2549 GLN ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2637 HIS ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A4065 GLN A4326 ASN ** A4381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.103707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083023 restraints weight = 63602.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.085718 restraints weight = 30442.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087489 restraints weight = 19376.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088615 restraints weight = 14530.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089302 restraints weight = 12120.323| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22292 Z= 0.143 Angle : 0.585 8.059 30248 Z= 0.291 Chirality : 0.041 0.198 3406 Planarity : 0.005 0.073 3871 Dihedral : 6.380 89.186 3037 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 2.12 % Allowed : 24.36 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.16), residues: 2689 helix: 2.17 (0.13), residues: 1462 sheet: -0.23 (0.35), residues: 231 loop : 0.06 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2831 TYR 0.014 0.001 TYR A2496 PHE 0.025 0.001 PHE A2635 TRP 0.032 0.001 TRP A4105 HIS 0.006 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00318 (22292) covalent geometry : angle 0.58470 (30248) hydrogen bonds : bond 0.04237 ( 1244) hydrogen bonds : angle 4.69458 ( 3618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1656 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8267 (ttpt) REVERT: A 1729 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7170 (mmmt) REVERT: A 1922 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8323 (tp40) REVERT: A 2018 MET cc_start: 0.7685 (mtp) cc_final: 0.7296 (mtp) REVERT: A 2324 LEU cc_start: 0.8356 (mt) cc_final: 0.8104 (tp) REVERT: A 2342 MET cc_start: 0.8609 (mmm) cc_final: 0.8146 (mmt) REVERT: A 2464 GLN cc_start: 0.8752 (tp40) cc_final: 0.8445 (tm-30) REVERT: A 3540 ASN cc_start: 0.9160 (m-40) cc_final: 0.8547 (t0) REVERT: A 3683 ASP cc_start: 0.7918 (t0) cc_final: 0.7718 (t0) REVERT: A 3847 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7620 (tptp) REVERT: A 4095 MET cc_start: 0.8116 (tmm) cc_final: 0.7294 (tmm) REVERT: A 4259 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 4473 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7736 (tmm) REVERT: A 4615 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7570 (mtt90) outliers start: 51 outliers final: 28 residues processed: 292 average time/residue: 0.1401 time to fit residues: 67.6656 Evaluate side-chains 260 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1748 GLN Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2770 THR Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4286 CYS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4615 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 120 optimal weight: 5.9990 chunk 261 optimal weight: 0.0470 chunk 255 optimal weight: 4.9990 chunk 87 optimal weight: 0.0020 chunk 106 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 126 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A3843 ASN A4065 GLN A4381 HIS ** A4477 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.105979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085394 restraints weight = 63663.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088150 restraints weight = 30075.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089937 restraints weight = 18958.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.091103 restraints weight = 14166.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.091823 restraints weight = 11764.818| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22292 Z= 0.107 Angle : 0.561 8.113 30248 Z= 0.273 Chirality : 0.040 0.228 3406 Planarity : 0.004 0.066 3871 Dihedral : 6.058 79.376 3029 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.43 % Rotamer: Outliers : 2.25 % Allowed : 24.28 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.16), residues: 2689 helix: 2.23 (0.13), residues: 1473 sheet: -0.30 (0.34), residues: 226 loop : 0.11 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2831 TYR 0.015 0.001 TYR A2748 PHE 0.019 0.001 PHE A3513 TRP 0.034 0.001 TRP A4105 HIS 0.003 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00226 (22292) covalent geometry : angle 0.56127 (30248) hydrogen bonds : bond 0.03724 ( 1244) hydrogen bonds : angle 4.41428 ( 3618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1729 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7062 (mmmt) REVERT: A 1809 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 1922 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8298 (tp40) REVERT: A 2342 MET cc_start: 0.8475 (mmm) cc_final: 0.8019 (mmt) REVERT: A 2779 MET cc_start: 0.8483 (mtp) cc_final: 0.8242 (mtp) REVERT: A 2804 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7720 (mtt180) REVERT: A 2867 MET cc_start: 0.6458 (pmm) cc_final: 0.5756 (pmm) REVERT: A 3005 LEU cc_start: 0.9323 (tp) cc_final: 0.9086 (tt) REVERT: A 3094 PHE cc_start: 0.8879 (t80) cc_final: 0.8401 (t80) REVERT: A 3126 MET cc_start: 0.5110 (mpp) cc_final: 0.4738 (mpp) REVERT: A 3176 TYR cc_start: 0.9269 (t80) cc_final: 0.9034 (t80) REVERT: A 3540 ASN cc_start: 0.9134 (m-40) cc_final: 0.8792 (m110) REVERT: A 3683 ASP cc_start: 0.7872 (t0) cc_final: 0.7634 (t0) REVERT: A 3847 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7643 (tptp) REVERT: A 4007 MET cc_start: 0.8704 (tpp) cc_final: 0.8270 (mtt) REVERT: A 4095 MET cc_start: 0.7930 (tmm) cc_final: 0.6975 (tmm) REVERT: A 4393 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7027 (tp40) REVERT: A 4454 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: A 4473 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7706 (tmm) REVERT: A 4615 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7310 (mtt90) outliers start: 54 outliers final: 27 residues processed: 324 average time/residue: 0.1371 time to fit residues: 72.7819 Evaluate side-chains 273 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1748 GLN Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4615 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 97 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 246 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2637 HIS ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3843 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.103285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082596 restraints weight = 64326.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085286 restraints weight = 30612.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087033 restraints weight = 19394.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088171 restraints weight = 14537.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088858 restraints weight = 12114.751| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22292 Z= 0.168 Angle : 0.586 7.975 30248 Z= 0.289 Chirality : 0.041 0.237 3406 Planarity : 0.004 0.061 3871 Dihedral : 5.893 73.305 3029 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 3.21 % Allowed : 24.32 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 2689 helix: 2.19 (0.13), residues: 1467 sheet: -0.39 (0.35), residues: 222 loop : 0.09 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2836 TYR 0.018 0.001 TYR A2638 PHE 0.047 0.001 PHE A2926 TRP 0.029 0.001 TRP A4105 HIS 0.007 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00384 (22292) covalent geometry : angle 0.58582 (30248) hydrogen bonds : bond 0.03732 ( 1244) hydrogen bonds : angle 4.40058 ( 3618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1729 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7162 (mmmt) REVERT: A 1922 GLN cc_start: 0.8707 (tp40) cc_final: 0.8417 (tp40) REVERT: A 2018 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7268 (mtp) REVERT: A 2324 LEU cc_start: 0.8020 (tp) cc_final: 0.7714 (mt) REVERT: A 2342 MET cc_start: 0.8488 (mmm) cc_final: 0.8287 (mmt) REVERT: A 2804 ARG cc_start: 0.8095 (mtm180) cc_final: 0.7768 (mtt180) REVERT: A 3005 LEU cc_start: 0.9357 (tp) cc_final: 0.9122 (tt) REVERT: A 3008 MET cc_start: 0.9290 (mmm) cc_final: 0.9072 (mmm) REVERT: A 3126 MET cc_start: 0.5170 (mpp) cc_final: 0.4709 (mpp) REVERT: A 3193 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 3540 ASN cc_start: 0.9156 (m-40) cc_final: 0.8572 (t0) REVERT: A 3683 ASP cc_start: 0.7984 (t0) cc_final: 0.7751 (t0) REVERT: A 3847 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7586 (tptp) REVERT: A 4095 MET cc_start: 0.7868 (tmm) cc_final: 0.6878 (tmm) REVERT: A 4393 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7131 (tp40) REVERT: A 4473 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7705 (tmm) REVERT: A 4615 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7642 (mtt90) outliers start: 77 outliers final: 46 residues processed: 306 average time/residue: 0.1343 time to fit residues: 68.5907 Evaluate side-chains 281 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1748 GLN Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4615 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 226 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 233 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 190 optimal weight: 0.0030 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 HIS A3622 ASN A4065 GLN A4477 GLN A4526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.105356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084555 restraints weight = 64136.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087287 restraints weight = 30862.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089076 restraints weight = 19689.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090236 restraints weight = 14789.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090945 restraints weight = 12330.250| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22292 Z= 0.108 Angle : 0.566 11.041 30248 Z= 0.272 Chirality : 0.040 0.183 3406 Planarity : 0.004 0.063 3871 Dihedral : 5.633 66.413 3029 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 3.04 % Allowed : 24.61 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.17), residues: 2689 helix: 2.27 (0.13), residues: 1470 sheet: -0.42 (0.33), residues: 237 loop : 0.10 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2863 TYR 0.020 0.001 TYR A2794 PHE 0.036 0.001 PHE A2926 TRP 0.020 0.001 TRP A4105 HIS 0.007 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00236 (22292) covalent geometry : angle 0.56626 (30248) hydrogen bonds : bond 0.03498 ( 1244) hydrogen bonds : angle 4.21574 ( 3618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1729 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7100 (mmmt) REVERT: A 1782 LEU cc_start: 0.8808 (tt) cc_final: 0.8440 (mt) REVERT: A 1809 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 1922 GLN cc_start: 0.8654 (tp40) cc_final: 0.8375 (tp40) REVERT: A 2018 MET cc_start: 0.7451 (mtp) cc_final: 0.7225 (mtp) REVERT: A 2324 LEU cc_start: 0.7916 (tp) cc_final: 0.7617 (mt) REVERT: A 2333 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 2779 MET cc_start: 0.8465 (mtp) cc_final: 0.8161 (mtp) REVERT: A 2804 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7698 (mtt180) REVERT: A 2867 MET cc_start: 0.7191 (pmm) cc_final: 0.6365 (pmm) REVERT: A 2995 ASP cc_start: 0.9066 (m-30) cc_final: 0.8388 (t70) REVERT: A 3005 LEU cc_start: 0.9322 (tp) cc_final: 0.9096 (tt) REVERT: A 3008 MET cc_start: 0.9303 (mmm) cc_final: 0.9081 (mmp) REVERT: A 3094 PHE cc_start: 0.8823 (t80) cc_final: 0.8361 (t80) REVERT: A 3176 TYR cc_start: 0.9295 (t80) cc_final: 0.9026 (t80) REVERT: A 3540 ASN cc_start: 0.9120 (m-40) cc_final: 0.8535 (t0) REVERT: A 3683 ASP cc_start: 0.7993 (t0) cc_final: 0.7705 (t0) REVERT: A 3711 GLN cc_start: 0.8250 (mt0) cc_final: 0.7957 (tm-30) REVERT: A 3967 GLU cc_start: 0.8691 (pm20) cc_final: 0.8483 (pm20) REVERT: A 4007 MET cc_start: 0.8673 (tpp) cc_final: 0.8301 (mtt) REVERT: A 4095 MET cc_start: 0.7794 (tmm) cc_final: 0.6764 (tmm) REVERT: A 4393 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7077 (tp40) REVERT: A 4473 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7753 (tmm) outliers start: 73 outliers final: 46 residues processed: 330 average time/residue: 0.1312 time to fit residues: 72.1301 Evaluate side-chains 295 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1748 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 195 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.104592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084043 restraints weight = 64041.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086760 restraints weight = 30474.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088485 restraints weight = 19242.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089645 restraints weight = 14425.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090327 restraints weight = 11985.326| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22292 Z= 0.124 Angle : 0.573 10.524 30248 Z= 0.276 Chirality : 0.040 0.207 3406 Planarity : 0.004 0.063 3871 Dihedral : 5.493 59.527 3029 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 2.71 % Allowed : 25.57 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.17), residues: 2689 helix: 2.25 (0.13), residues: 1470 sheet: -0.41 (0.34), residues: 235 loop : 0.14 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2863 TYR 0.020 0.001 TYR A2638 PHE 0.024 0.001 PHE A2926 TRP 0.019 0.001 TRP A4105 HIS 0.006 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00283 (22292) covalent geometry : angle 0.57259 (30248) hydrogen bonds : bond 0.03487 ( 1244) hydrogen bonds : angle 4.22346 ( 3618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1729 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7225 (mmmm) REVERT: A 1782 LEU cc_start: 0.8837 (tt) cc_final: 0.8455 (mt) REVERT: A 1922 GLN cc_start: 0.8692 (tp40) cc_final: 0.8397 (tp40) REVERT: A 2324 LEU cc_start: 0.7948 (tp) cc_final: 0.7613 (mt) REVERT: A 2333 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 2779 MET cc_start: 0.8440 (mtp) cc_final: 0.7965 (mtp) REVERT: A 2867 MET cc_start: 0.7163 (pmm) cc_final: 0.6259 (pmm) REVERT: A 2887 GLU cc_start: 0.7937 (mp0) cc_final: 0.7635 (mp0) REVERT: A 3005 LEU cc_start: 0.9278 (tp) cc_final: 0.9071 (tt) REVERT: A 3008 MET cc_start: 0.9323 (mmm) cc_final: 0.9040 (mmm) REVERT: A 3043 MET cc_start: 0.8055 (pmm) cc_final: 0.7818 (pmm) REVERT: A 3094 PHE cc_start: 0.8844 (t80) cc_final: 0.8355 (t80) REVERT: A 3126 MET cc_start: 0.5077 (mpp) cc_final: 0.4691 (mpp) REVERT: A 3176 TYR cc_start: 0.9308 (t80) cc_final: 0.9041 (t80) REVERT: A 3540 ASN cc_start: 0.9133 (m-40) cc_final: 0.8582 (t0) REVERT: A 3683 ASP cc_start: 0.8009 (t0) cc_final: 0.7716 (t0) REVERT: A 3711 GLN cc_start: 0.8269 (mt0) cc_final: 0.8032 (tm-30) REVERT: A 4095 MET cc_start: 0.7755 (tmm) cc_final: 0.6693 (tmm) REVERT: A 4393 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7158 (tp40) REVERT: A 4473 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7749 (tmm) outliers start: 65 outliers final: 55 residues processed: 308 average time/residue: 0.1279 time to fit residues: 65.9652 Evaluate side-chains 306 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1729 LYS Chi-restraints excluded: chain A residue 1748 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3851 ASP Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 86 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 198 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 219 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087380 restraints weight = 65561.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090058 restraints weight = 31524.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091852 restraints weight = 20010.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093013 restraints weight = 14978.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093615 restraints weight = 12464.673| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22292 Z= 0.108 Angle : 0.584 11.094 30248 Z= 0.279 Chirality : 0.040 0.199 3406 Planarity : 0.004 0.065 3871 Dihedral : 5.357 57.076 3029 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.62 % Allowed : 25.86 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.17), residues: 2689 helix: 2.29 (0.13), residues: 1470 sheet: -0.41 (0.33), residues: 245 loop : 0.16 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2831 TYR 0.016 0.001 TYR A3026 PHE 0.014 0.001 PHE A2682 TRP 0.029 0.001 TRP A4105 HIS 0.005 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00239 (22292) covalent geometry : angle 0.58416 (30248) hydrogen bonds : bond 0.03384 ( 1244) hydrogen bonds : angle 4.16917 ( 3618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1782 LEU cc_start: 0.8829 (tt) cc_final: 0.8447 (mt) REVERT: A 1922 GLN cc_start: 0.8694 (tp40) cc_final: 0.8408 (tp40) REVERT: A 2324 LEU cc_start: 0.7976 (tp) cc_final: 0.7649 (mt) REVERT: A 2333 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7856 (mm) REVERT: A 2342 MET cc_start: 0.8318 (mmm) cc_final: 0.7744 (mmt) REVERT: A 2603 MET cc_start: 0.8724 (mmp) cc_final: 0.8481 (mmm) REVERT: A 2779 MET cc_start: 0.8458 (mtp) cc_final: 0.8101 (mtp) REVERT: A 2887 GLU cc_start: 0.7924 (mp0) cc_final: 0.7634 (mp0) REVERT: A 3008 MET cc_start: 0.9349 (mmm) cc_final: 0.9070 (mmm) REVERT: A 3094 PHE cc_start: 0.8816 (t80) cc_final: 0.8389 (t80) REVERT: A 3126 MET cc_start: 0.5035 (mpp) cc_final: 0.4599 (mpp) REVERT: A 3176 TYR cc_start: 0.9272 (t80) cc_final: 0.9035 (t80) REVERT: A 3540 ASN cc_start: 0.9119 (m-40) cc_final: 0.8813 (m-40) REVERT: A 3586 TYR cc_start: 0.8577 (m-80) cc_final: 0.8321 (m-80) REVERT: A 3683 ASP cc_start: 0.8040 (t0) cc_final: 0.7754 (t0) REVERT: A 3711 GLN cc_start: 0.8267 (mt0) cc_final: 0.7970 (tm-30) REVERT: A 4095 MET cc_start: 0.7669 (tmm) cc_final: 0.6546 (tmm) REVERT: A 4393 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7209 (tp40) REVERT: A 4473 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7683 (tmm) outliers start: 63 outliers final: 46 residues processed: 316 average time/residue: 0.1326 time to fit residues: 70.4451 Evaluate side-chains 307 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4286 CYS Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 47 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 171 optimal weight: 0.0070 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3602 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.104992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084504 restraints weight = 63963.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087172 restraints weight = 30691.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088934 restraints weight = 19487.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090047 restraints weight = 14586.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090744 restraints weight = 12144.435| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22292 Z= 0.112 Angle : 0.580 9.859 30248 Z= 0.279 Chirality : 0.040 0.184 3406 Planarity : 0.004 0.064 3871 Dihedral : 5.193 53.526 3027 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 2.71 % Allowed : 25.70 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.17), residues: 2689 helix: 2.31 (0.13), residues: 1475 sheet: -0.40 (0.33), residues: 245 loop : 0.17 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A2831 TYR 0.014 0.001 TYR A3026 PHE 0.061 0.001 PHE A2926 TRP 0.032 0.001 TRP A4105 HIS 0.004 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00254 (22292) covalent geometry : angle 0.58030 (30248) hydrogen bonds : bond 0.03387 ( 1244) hydrogen bonds : angle 4.14137 ( 3618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 262 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1782 LEU cc_start: 0.8843 (tt) cc_final: 0.8470 (mt) REVERT: A 1922 GLN cc_start: 0.8717 (tp40) cc_final: 0.8423 (tp40) REVERT: A 2342 MET cc_start: 0.8339 (mmm) cc_final: 0.7751 (mmt) REVERT: A 2603 MET cc_start: 0.8745 (mmp) cc_final: 0.8506 (mmm) REVERT: A 2867 MET cc_start: 0.7176 (pmm) cc_final: 0.6411 (pmm) REVERT: A 2887 GLU cc_start: 0.7911 (mp0) cc_final: 0.7640 (mp0) REVERT: A 2953 MET cc_start: 0.8562 (ppp) cc_final: 0.8286 (ppp) REVERT: A 2995 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8064 (t70) REVERT: A 3094 PHE cc_start: 0.8832 (t80) cc_final: 0.8399 (t80) REVERT: A 3126 MET cc_start: 0.5098 (mpp) cc_final: 0.4676 (mpp) REVERT: A 3176 TYR cc_start: 0.9281 (t80) cc_final: 0.9058 (t80) REVERT: A 3540 ASN cc_start: 0.9118 (m-40) cc_final: 0.8817 (m-40) REVERT: A 3586 TYR cc_start: 0.8599 (m-80) cc_final: 0.8352 (m-80) REVERT: A 3683 ASP cc_start: 0.8036 (t0) cc_final: 0.7759 (t0) REVERT: A 3711 GLN cc_start: 0.8294 (mt0) cc_final: 0.8023 (tm-30) REVERT: A 4095 MET cc_start: 0.7690 (tmm) cc_final: 0.6575 (tmm) REVERT: A 4393 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7201 (tp40) REVERT: A 4473 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7684 (tmm) outliers start: 65 outliers final: 49 residues processed: 306 average time/residue: 0.1256 time to fit residues: 65.4359 Evaluate side-chains 303 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4286 CYS Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.105083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084516 restraints weight = 64231.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087181 restraints weight = 30621.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088953 restraints weight = 19483.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090061 restraints weight = 14543.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090807 restraints weight = 12104.956| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22292 Z= 0.114 Angle : 0.598 9.703 30248 Z= 0.286 Chirality : 0.041 0.195 3406 Planarity : 0.004 0.064 3871 Dihedral : 5.132 52.178 3027 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 26.07 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.17), residues: 2689 helix: 2.32 (0.13), residues: 1467 sheet: -0.43 (0.33), residues: 245 loop : 0.21 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2831 TYR 0.015 0.001 TYR A2638 PHE 0.046 0.001 PHE A2926 TRP 0.035 0.001 TRP A4105 HIS 0.004 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00257 (22292) covalent geometry : angle 0.59837 (30248) hydrogen bonds : bond 0.03365 ( 1244) hydrogen bonds : angle 4.13503 ( 3618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1632 VAL cc_start: 0.8652 (m) cc_final: 0.8285 (m) REVERT: A 1782 LEU cc_start: 0.8845 (tt) cc_final: 0.8471 (mt) REVERT: A 1922 GLN cc_start: 0.8720 (tp40) cc_final: 0.8433 (tp40) REVERT: A 1938 PHE cc_start: 0.7865 (t80) cc_final: 0.7576 (m-80) REVERT: A 2342 MET cc_start: 0.8369 (mmm) cc_final: 0.7808 (mmt) REVERT: A 2779 MET cc_start: 0.8734 (mtp) cc_final: 0.8419 (mtp) REVERT: A 2887 GLU cc_start: 0.7933 (mp0) cc_final: 0.7664 (mp0) REVERT: A 2953 MET cc_start: 0.8567 (ppp) cc_final: 0.8322 (ppp) REVERT: A 2995 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.7974 (t70) REVERT: A 3094 PHE cc_start: 0.8843 (t80) cc_final: 0.8422 (t80) REVERT: A 3176 TYR cc_start: 0.9283 (t80) cc_final: 0.9072 (t80) REVERT: A 3540 ASN cc_start: 0.9099 (m-40) cc_final: 0.8810 (m-40) REVERT: A 3586 TYR cc_start: 0.8592 (m-80) cc_final: 0.8336 (m-80) REVERT: A 3683 ASP cc_start: 0.8037 (t0) cc_final: 0.7769 (t0) REVERT: A 3711 GLN cc_start: 0.8300 (mt0) cc_final: 0.8009 (tm-30) REVERT: A 3847 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7609 (tptp) REVERT: A 4095 MET cc_start: 0.7687 (tmm) cc_final: 0.6563 (tmm) REVERT: A 4393 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7177 (tp40) REVERT: A 4473 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7680 (tmm) outliers start: 60 outliers final: 53 residues processed: 306 average time/residue: 0.1373 time to fit residues: 69.5398 Evaluate side-chains 310 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3623 LEU Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 61 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 chunk 259 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.104709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083764 restraints weight = 64703.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086460 restraints weight = 31621.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088213 restraints weight = 20262.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089310 restraints weight = 15299.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090049 restraints weight = 12838.935| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22292 Z= 0.124 Angle : 0.616 11.890 30248 Z= 0.293 Chirality : 0.041 0.182 3406 Planarity : 0.004 0.064 3871 Dihedral : 5.118 49.801 3027 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.37 % Allowed : 26.57 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.17), residues: 2689 helix: 2.28 (0.13), residues: 1478 sheet: -0.47 (0.33), residues: 247 loop : 0.23 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A2831 TYR 0.022 0.001 TYR A2638 PHE 0.049 0.001 PHE A2926 TRP 0.037 0.001 TRP A4105 HIS 0.004 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00284 (22292) covalent geometry : angle 0.61551 (30248) hydrogen bonds : bond 0.03406 ( 1244) hydrogen bonds : angle 4.14319 ( 3618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1782 LEU cc_start: 0.8846 (tt) cc_final: 0.8474 (mt) REVERT: A 1922 GLN cc_start: 0.8705 (tp40) cc_final: 0.8418 (tp40) REVERT: A 2324 LEU cc_start: 0.8324 (mt) cc_final: 0.8071 (tp) REVERT: A 2342 MET cc_start: 0.8433 (mmm) cc_final: 0.7860 (mmt) REVERT: A 2953 MET cc_start: 0.8551 (ppp) cc_final: 0.8293 (ppp) REVERT: A 3008 MET cc_start: 0.9378 (mmm) cc_final: 0.9157 (mmm) REVERT: A 3126 MET cc_start: 0.4861 (mpp) cc_final: 0.4565 (mpp) REVERT: A 3176 TYR cc_start: 0.9292 (t80) cc_final: 0.9084 (t80) REVERT: A 3540 ASN cc_start: 0.9099 (m-40) cc_final: 0.8833 (m-40) REVERT: A 3586 TYR cc_start: 0.8617 (m-80) cc_final: 0.8367 (m-80) REVERT: A 3683 ASP cc_start: 0.8051 (t0) cc_final: 0.7787 (t0) REVERT: A 3711 GLN cc_start: 0.8313 (mt0) cc_final: 0.8068 (tm-30) REVERT: A 4095 MET cc_start: 0.7723 (tmm) cc_final: 0.6620 (tmm) REVERT: A 4393 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7184 (tp40) REVERT: A 4473 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7702 (tmm) outliers start: 57 outliers final: 51 residues processed: 293 average time/residue: 0.1315 time to fit residues: 65.4607 Evaluate side-chains 298 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2254 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3623 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3808 CYS Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4309 VAL Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 206 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2171 HIS ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.105154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084522 restraints weight = 64345.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087212 restraints weight = 30814.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088983 restraints weight = 19583.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090138 restraints weight = 14623.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090842 restraints weight = 12127.049| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22292 Z= 0.115 Angle : 0.611 11.759 30248 Z= 0.291 Chirality : 0.041 0.177 3406 Planarity : 0.004 0.064 3871 Dihedral : 5.089 49.644 3027 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 2.37 % Allowed : 26.32 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.17), residues: 2689 helix: 2.30 (0.13), residues: 1471 sheet: -0.43 (0.33), residues: 247 loop : 0.23 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2831 TYR 0.018 0.001 TYR A2638 PHE 0.042 0.001 PHE A2926 TRP 0.039 0.001 TRP A4105 HIS 0.004 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00263 (22292) covalent geometry : angle 0.61133 (30248) hydrogen bonds : bond 0.03374 ( 1244) hydrogen bonds : angle 4.12108 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.37 seconds wall clock time: 74 minutes 53.86 seconds (4493.86 seconds total)