Starting phenix.real_space_refine on Thu May 22 01:40:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.map" model { file = "/net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dh8_46859/05_2025/9dh8_46859.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 111 5.16 5 C 13881 2.51 5 N 3772 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21847 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2709, 21735 Classifications: {'peptide': 2709} Link IDs: {'PTRANS': 126, 'TRANS': 2582} Chain breaks: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.77, per 1000 atoms: 0.54 Number of scatterers: 21847 At special positions: 0 Unit cell: (108.786, 165.494, 150.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4074 8.00 N 3772 7.00 C 13881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.5 seconds 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 17 sheets defined 61.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1649 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.530A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.913A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 removed outlier: 3.847A pdb=" N VAL A1916 " --> pdb=" O LYS A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.743A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.619A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2133 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.349A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2190 removed outlier: 3.597A pdb=" N GLU A2180 " --> pdb=" O THR A2176 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.607A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2316 removed outlier: 3.632A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.687A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.625A 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 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2548 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.574A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.690A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2628 through 2638 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: 5.265A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.683A pdb=" N MET A2779 " --> pdb=" O GLU A2775 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A2784 " --> pdb=" O SER A2780 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.670A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2928 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: 3.962A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 removed outlier: 3.645A pdb=" N ARG A3088 " --> pdb=" O ALA A3084 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3219 removed outlier: 3.782A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A3196 " --> pdb=" O SER A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 5.010A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.896A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.721A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 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: 3.535A pdb=" N CYS A3693 " --> pdb=" O PRO A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3737 removed outlier: 4.036A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3737 through 3755 removed outlier: 3.542A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3791 Processing helix chain 'A' and resid 3793 through 3801 removed outlier: 3.708A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 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 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 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 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.141A 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 removed outlier: 3.556A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.125A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.716A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.751A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.345A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.746A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A4170 " --> pdb=" O VAL A4166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4165 through 4170' Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.267A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.502A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.708A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4407 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 3.861A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4532 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: 3.688A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 3.508A pdb=" N LEU A1928 " --> pdb=" O TRP A1954 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 6.741A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (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 removed outlier: 3.511A pdb=" N LEU A2325 " --> pdb=" O LEU A2333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A2333 " --> pdb=" O LEU A2325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2540 removed outlier: 3.832A pdb=" N GLU A2544 " --> pdb=" O SER A2540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2617 through 2620 removed outlier: 5.897A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.941A 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 removed outlier: 3.535A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.073A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.207A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.285A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 3.537A pdb=" N THR A4561 " --> pdb=" O VAL A4509 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.861A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.69 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7177 1.34 - 1.46: 3378 1.46 - 1.58: 11567 1.58 - 1.69: 13 1.69 - 1.81: 185 Bond restraints: 22320 Sorted by residual: bond pdb=" CG LEU A1811 " pdb=" CD2 LEU A1811 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CB PRO A2020 " pdb=" CG PRO A2020 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.00e+00 bond pdb=" CG1 ILE A2498 " pdb=" CD1 ILE A2498 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.35e+00 bond pdb=" C MET A2222 " pdb=" N VAL A2223 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.26e-02 6.30e+03 2.26e+00 bond pdb=" CB ILE A3767 " pdb=" CG2 ILE A3767 " ideal model delta sigma weight residual 1.521 1.564 -0.043 3.30e-02 9.18e+02 1.72e+00 ... (remaining 22315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 29998 2.78 - 5.56: 257 5.56 - 8.34: 25 8.34 - 11.12: 1 11.12 - 13.90: 1 Bond angle restraints: 30282 Sorted by residual: angle pdb=" C ALA A1862 " pdb=" CA ALA A1862 " pdb=" CB ALA A1862 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N MET A3791 " pdb=" CA MET A3791 " pdb=" C MET A3791 " ideal model delta sigma weight residual 113.20 107.28 5.92 1.21e+00 6.83e-01 2.40e+01 angle pdb=" CA LEU A4311 " pdb=" CB LEU A4311 " pdb=" CG LEU A4311 " ideal model delta sigma weight residual 116.30 130.20 -13.90 3.50e+00 8.16e-02 1.58e+01 angle pdb=" C ASN A3498 " pdb=" N GLN A3499 " pdb=" CA GLN A3499 " ideal model delta sigma weight residual 121.14 115.18 5.96 1.75e+00 3.27e-01 1.16e+01 angle pdb=" N GLN A2834 " pdb=" CA GLN A2834 " pdb=" C GLN A2834 " ideal model delta sigma weight residual 114.75 110.80 3.95 1.26e+00 6.30e-01 9.84e+00 ... (remaining 30277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 13092 30.36 - 60.72: 381 60.72 - 91.08: 53 91.08 - 121.44: 1 121.44 - 151.80: 1 Dihedral angle restraints: 13528 sinusoidal: 5604 harmonic: 7924 Sorted by residual: dihedral pdb=" C2' ADP A4701 " pdb=" C1' ADP A4701 " pdb=" N9 ADP A4701 " pdb=" C4 ADP A4701 " ideal model delta sinusoidal sigma weight residual 91.55 -116.65 -151.80 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 37.94 -97.95 1 2.00e+01 2.50e-03 2.73e+01 dihedral pdb=" C2' ADP A4703 " pdb=" C1' ADP A4703 " pdb=" N9 ADP A4703 " pdb=" C4 ADP A4703 " ideal model delta sinusoidal sigma weight residual 91.55 5.09 86.46 1 2.00e+01 2.50e-03 2.25e+01 ... (remaining 13525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2567 0.043 - 0.087: 655 0.087 - 0.130: 174 0.130 - 0.173: 12 0.173 - 0.217: 2 Chirality restraints: 3410 Sorted by residual: chirality pdb=" CB ILE A2747 " pdb=" CA ILE A2747 " pdb=" CG1 ILE A2747 " pdb=" CG2 ILE A2747 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A1698 " pdb=" CA ILE A1698 " pdb=" CG1 ILE A1698 " pdb=" CG2 ILE A1698 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CG LEU A3750 " pdb=" CB LEU A3750 " pdb=" CD1 LEU A3750 " pdb=" CD2 LEU A3750 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 3407 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A3672 " 0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A3673 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A3673 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A3673 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A3137 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A2738 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO A2739 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2739 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2739 " 0.026 5.00e-02 4.00e+02 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 300 2.67 - 3.22: 21939 3.22 - 3.78: 35287 3.78 - 4.34: 46667 4.34 - 4.90: 75765 Nonbonded interactions: 179958 Sorted by model distance: nonbonded pdb=" OG1 THR A1913 " pdb=" O1A ADP A4701 " model vdw 2.108 3.040 nonbonded pdb=" OH TYR A2086 " pdb=" OD2 ASP A2153 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR A4205 " pdb=" OD2 ASP A4261 " model vdw 2.158 3.040 nonbonded pdb=" OE2 GLU A3485 " pdb=" NE1 TRP A3489 " model vdw 2.193 3.120 nonbonded pdb=" O ILE A2253 " pdb=" OH TYR A2693 " model vdw 2.201 3.040 ... (remaining 179953 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=1.00 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 51.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 0.087 22320 Z= 0.181 Angle : 0.657 13.896 30282 Z= 0.341 Chirality : 0.041 0.217 3410 Planarity : 0.004 0.057 3879 Dihedral : 14.593 151.802 8380 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2697 helix: 1.74 (0.13), residues: 1518 sheet: -1.11 (0.32), residues: 249 loop : 0.21 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A3093 HIS 0.013 0.001 HIS A1921 PHE 0.026 0.002 PHE A4268 TYR 0.022 0.002 TYR A1738 ARG 0.006 0.001 ARG A1628 Details of bonding type rmsd hydrogen bonds : bond 0.14269 ( 1247) hydrogen bonds : angle 5.87261 ( 3639) covalent geometry : bond 0.00415 (22320) covalent geometry : angle 0.65695 (30282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1677 SER cc_start: 0.8613 (t) cc_final: 0.8286 (p) REVERT: A 1680 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6696 (tp30) REVERT: A 1704 LEU cc_start: 0.7987 (mt) cc_final: 0.7612 (mm) REVERT: A 1769 MET cc_start: 0.6646 (mmp) cc_final: 0.6146 (mmm) REVERT: A 1945 PHE cc_start: 0.7637 (t80) cc_final: 0.7425 (t80) REVERT: A 1976 GLN cc_start: 0.8142 (tt0) cc_final: 0.7645 (tt0) REVERT: A 2175 MET cc_start: 0.8059 (mpp) cc_final: 0.7149 (mtp) REVERT: A 2345 VAL cc_start: 0.8589 (p) cc_final: 0.8375 (m) REVERT: A 2447 MET cc_start: 0.8337 (mtp) cc_final: 0.8001 (mtt) REVERT: A 3030 MET cc_start: 0.6503 (mmm) cc_final: 0.5624 (mmp) REVERT: A 3576 ASN cc_start: 0.8202 (m-40) cc_final: 0.7915 (m-40) REVERT: A 3613 SER cc_start: 0.7941 (t) cc_final: 0.6747 (p) REVERT: A 3623 LEU cc_start: 0.7751 (tp) cc_final: 0.7468 (tt) REVERT: A 3692 LEU cc_start: 0.8073 (mm) cc_final: 0.7558 (mt) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.4338 time to fit residues: 354.8808 Evaluate side-chains 270 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.7980 chunk 204 optimal weight: 0.0970 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 245 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN A2187 GLN A2252 HIS ** A2621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3032 GLN ** A3047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 ASN A3538 GLN A3800 GLN A3845 ASN A4526 GLN A4566 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.145514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113104 restraints weight = 41422.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116146 restraints weight = 24168.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118123 restraints weight = 17443.772| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22320 Z= 0.136 Angle : 0.603 7.995 30282 Z= 0.301 Chirality : 0.041 0.189 3410 Planarity : 0.005 0.048 3879 Dihedral : 6.881 154.748 3009 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.91 % Allowed : 9.11 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.16), residues: 2697 helix: 1.80 (0.13), residues: 1535 sheet: -1.02 (0.32), residues: 246 loop : 0.24 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.011 0.001 HIS A1921 PHE 0.025 0.002 PHE A2912 TYR 0.023 0.001 TYR A2693 ARG 0.007 0.001 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1247) hydrogen bonds : angle 4.61725 ( 3639) covalent geometry : bond 0.00302 (22320) covalent geometry : angle 0.60289 (30282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 312 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1677 SER cc_start: 0.8391 (t) cc_final: 0.7973 (p) REVERT: A 1680 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6661 (tp30) REVERT: A 1928 LEU cc_start: 0.7688 (mm) cc_final: 0.7485 (mm) REVERT: A 1941 MET cc_start: 0.8077 (tmm) cc_final: 0.7843 (tmm) REVERT: A 2175 MET cc_start: 0.7764 (mpp) cc_final: 0.7245 (mtt) REVERT: A 2345 VAL cc_start: 0.8530 (p) cc_final: 0.8308 (m) REVERT: A 2488 ARG cc_start: 0.6050 (mtm110) cc_final: 0.5824 (mtm110) REVERT: A 2603 MET cc_start: 0.7539 (ppp) cc_final: 0.7182 (ppp) REVERT: A 2683 ILE cc_start: 0.8437 (pt) cc_final: 0.8235 (tt) REVERT: A 2933 LEU cc_start: 0.8150 (mt) cc_final: 0.7925 (mt) REVERT: A 2987 ASN cc_start: 0.7273 (t0) cc_final: 0.6862 (m-40) REVERT: A 2994 MET cc_start: 0.8010 (tpp) cc_final: 0.7700 (tpp) REVERT: A 3129 VAL cc_start: 0.8134 (m) cc_final: 0.7788 (p) REVERT: A 3962 ASP cc_start: 0.8345 (t0) cc_final: 0.7993 (t0) REVERT: A 4416 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6061 (mm-30) REVERT: A 4436 GLN cc_start: 0.8346 (tp40) cc_final: 0.8060 (tp40) REVERT: A 4451 LEU cc_start: 0.8191 (tt) cc_final: 0.7797 (mt) outliers start: 22 outliers final: 10 residues processed: 328 average time/residue: 0.3627 time to fit residues: 183.7766 Evaluate side-chains 260 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 2878 SER Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3584 ASN Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2787 > 50: distance: 50 - 55: 20.581 distance: 55 - 56: 8.974 distance: 56 - 57: 27.275 distance: 56 - 59: 4.831 distance: 57 - 58: 34.976 distance: 57 - 63: 15.621 distance: 59 - 60: 12.780 distance: 60 - 61: 16.051 distance: 61 - 62: 3.907 distance: 63 - 64: 21.709 distance: 64 - 65: 9.743 distance: 64 - 67: 13.894 distance: 65 - 66: 20.707 distance: 65 - 71: 13.877 distance: 67 - 68: 4.768 distance: 68 - 69: 15.236 distance: 68 - 70: 21.257 distance: 71 - 72: 10.492 distance: 71 - 77: 3.681 distance: 72 - 73: 6.453 distance: 72 - 75: 6.899 distance: 73 - 74: 11.585 distance: 73 - 78: 4.744 distance: 75 - 76: 5.829 distance: 76 - 77: 12.003 distance: 78 - 79: 9.405 distance: 79 - 80: 13.538 distance: 79 - 82: 4.818 distance: 80 - 81: 7.542 distance: 80 - 84: 21.074 distance: 81 - 103: 18.097 distance: 82 - 83: 10.896 distance: 84 - 85: 7.608 distance: 85 - 86: 19.799 distance: 85 - 88: 9.031 distance: 86 - 87: 29.284 distance: 86 - 90: 10.455 distance: 87 - 111: 14.446 distance: 88 - 89: 12.898 distance: 90 - 91: 9.840 distance: 91 - 92: 8.314 distance: 91 - 94: 4.465 distance: 92 - 93: 16.269 distance: 92 - 99: 23.820 distance: 93 - 120: 10.355 distance: 94 - 95: 5.500 distance: 96 - 97: 4.896 distance: 96 - 98: 3.753 distance: 99 - 100: 6.919 distance: 100 - 101: 5.826 distance: 101 - 102: 4.869 distance: 101 - 103: 13.240 distance: 102 - 128: 10.815 distance: 103 - 104: 19.956 distance: 104 - 105: 6.669 distance: 104 - 107: 13.864 distance: 105 - 106: 23.590 distance: 105 - 111: 15.307 distance: 106 - 139: 10.620 distance: 107 - 108: 11.377 distance: 108 - 109: 6.279 distance: 108 - 110: 6.612 distance: 111 - 112: 9.782 distance: 112 - 113: 12.656 distance: 112 - 115: 16.726 distance: 113 - 114: 20.162 distance: 113 - 120: 7.724 distance: 114 - 144: 12.827 distance: 115 - 116: 22.663 distance: 116 - 117: 9.914 distance: 117 - 118: 6.710 distance: 120 - 121: 5.923 distance: 121 - 122: 9.478 distance: 121 - 124: 9.923 distance: 122 - 123: 5.913 distance: 122 - 128: 7.344 distance: 123 - 149: 7.635 distance: 124 - 125: 13.853 distance: 125 - 126: 14.088 distance: 125 - 127: 10.714