Starting phenix.real_space_refine on Sat May 24 04:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmw_44713/05_2025/9bmw_44713.cif" } resolution = 3.3 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= 0.031 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 15646 2.51 5 N 4254 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24617 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3043, 24503 Classifications: {'peptide': 3043} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2909} Chain breaks: 3 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 12.76, per 1000 atoms: 0.52 Number of scatterers: 24617 At special positions: 0 Unit cell: (171.179, 156.742, 127.869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 9 15.00 Mg 2 11.99 O 4584 8.00 N 4254 7.00 C 15646 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: 5.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 20 sheets defined 63.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1350 through 1354 Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.629A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1472 removed outlier: 3.710A pdb=" N THR A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.733A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1515 removed outlier: 5.087A pdb=" N TYR A1512 " --> pdb=" O LEU A1509 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1515 " --> pdb=" O TYR A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.862A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 removed outlier: 3.508A pdb=" N SER A1600 " --> pdb=" O GLY A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.720A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.544A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.823A 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 1773 removed outlier: 3.731A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.753A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.551A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (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 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.611A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 Processing helix chain 'A' and resid 2045 through 2056 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.584A 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 2132 through 2146 removed outlier: 3.619A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.088A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2314 through 2320 removed outlier: 4.324A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.521A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 4.093A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 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: 3.674A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.612A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) 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 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.736A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.641A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.000A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2757 removed outlier: 4.269A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.605A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.849A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2834 through 2837 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.733A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 3.541A pdb=" N ALA A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.555A pdb=" N LEU A2920 " --> pdb=" O LEU A2916 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2984 removed outlier: 3.547A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3002 through 3015 removed outlier: 3.856A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.538A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 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 3221 removed outlier: 3.649A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.880A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.684A 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: 3.648A 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 3651 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3706 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 4.180A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.502A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 removed outlier: 3.712A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) 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 3874 removed outlier: 3.582A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 6.287A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 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 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.683A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.880A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.506A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.641A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.519A 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 removed outlier: 4.010A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.991A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.654A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.554A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.177A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.573A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4348 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4403 through 4406 removed outlier: 3.710A pdb=" N LYS A4406 " --> pdb=" O GLU A4403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4403 through 4406' 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 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.094A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.817A 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 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 1476 through 1480 removed outlier: 4.430A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 10.461A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.951A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 7.066A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2710 through 2712 removed outlier: 6.507A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.672A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.722A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.209A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 3.728A pdb=" N GLN A3636 " --> pdb=" O THR A3612 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.494A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.926A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.297A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4583 through 4584 removed outlier: 3.569A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4570 1440 hydrogen bonds defined for protein. 4197 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: 15.89 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6741 1.33 - 1.45: 4325 1.45 - 1.58: 13856 1.58 - 1.70: 14 1.70 - 1.82: 206 Bond restraints: 25142 Sorted by residual: bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N VAL A1563 " pdb=" CA VAL A1563 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N ILE A1571 " pdb=" CA ILE A1571 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.44e+00 bond pdb=" N ASP A1606 " pdb=" CA ASP A1606 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.26e+00 bond pdb=" N PHE A1568 " pdb=" CA PHE A1568 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.17e+00 ... (remaining 25137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 33451 2.14 - 4.27: 550 4.27 - 6.41: 76 6.41 - 8.54: 9 8.54 - 10.68: 3 Bond angle restraints: 34089 Sorted by residual: angle pdb=" C LYS A1409 " pdb=" CA LYS A1409 " pdb=" CB LYS A1409 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" CA LYS A1409 " pdb=" C LYS A1409 " pdb=" N ASP A1410 " ideal model delta sigma weight residual 119.98 116.90 3.08 8.50e-01 1.38e+00 1.31e+01 angle pdb=" CB MET A2953 " pdb=" CG MET A2953 " pdb=" SD MET A2953 " ideal model delta sigma weight residual 112.70 102.02 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C THR A3031 " pdb=" N GLN A3032 " pdb=" CA GLN A3032 " ideal model delta sigma weight residual 121.14 115.09 6.05 1.75e+00 3.27e-01 1.20e+01 angle pdb=" CB MET A3885 " pdb=" CG MET A3885 " pdb=" SD MET A3885 " ideal model delta sigma weight residual 112.70 102.66 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 34084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13626 17.96 - 35.92: 1311 35.92 - 53.88: 230 53.88 - 71.84: 69 71.84 - 89.80: 22 Dihedral angle restraints: 15258 sinusoidal: 6348 harmonic: 8910 Sorted by residual: dihedral pdb=" CA ARG A2507 " pdb=" C ARG A2507 " pdb=" N LEU A2508 " pdb=" CA LEU A2508 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP A3093 " pdb=" C TRP A3093 " pdb=" N PHE A3094 " pdb=" CA PHE A3094 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -123.58 63.59 1 2.00e+01 2.50e-03 1.33e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2949 0.045 - 0.090: 664 0.090 - 0.135: 191 0.135 - 0.180: 16 0.180 - 0.225: 1 Chirality restraints: 3821 Sorted by residual: chirality pdb=" CA ILE A1571 " pdb=" N ILE A1571 " pdb=" C ILE A1571 " pdb=" CB ILE A1571 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A1466 " pdb=" CA ILE A1466 " pdb=" CG1 ILE A1466 " pdb=" CG2 ILE A1466 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB THR A3685 " pdb=" CA THR A3685 " pdb=" OG1 THR A3685 " pdb=" CG2 THR A3685 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 3818 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A3093 " 0.017 2.00e-02 2.50e+03 1.83e-02 8.38e+00 pdb=" CG TRP A3093 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A3093 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A3093 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A3093 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3093 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A3093 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A2907 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A2908 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A2908 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A2908 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2825 " -0.015 2.00e-02 2.50e+03 1.23e-02 3.79e+00 pdb=" CG TRP A2825 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A2825 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A2825 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A2825 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A2825 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A2825 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2825 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2825 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A2825 " 0.001 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 164 2.55 - 3.14: 19892 3.14 - 3.73: 39987 3.73 - 4.31: 52072 4.31 - 4.90: 88691 Nonbonded interactions: 200806 Sorted by model distance: nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4706 " model vdw 1.967 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.986 2.170 nonbonded pdb=" OG SER A3593 " pdb=" OE1 GLN A3595 " model vdw 2.127 3.040 nonbonded pdb=" O ASP A4631 " pdb=" OG SER A4634 " model vdw 2.163 3.040 nonbonded pdb=" O THR A3028 " pdb=" OG1 THR A3031 " model vdw 2.179 3.040 ... (remaining 200801 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 59.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.120 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25142 Z= 0.163 Angle : 0.637 10.680 34089 Z= 0.335 Chirality : 0.041 0.225 3821 Planarity : 0.004 0.070 4367 Dihedral : 14.817 89.799 9470 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.71 (0.16), residues: 3035 helix: 1.90 (0.12), residues: 1748 sheet: -0.32 (0.38), residues: 213 loop : 0.29 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A3093 HIS 0.009 0.001 HIS A4119 PHE 0.027 0.002 PHE A1629 TYR 0.025 0.002 TYR A2748 ARG 0.011 0.001 ARG A2965 Details of bonding type rmsd hydrogen bonds : bond 0.12766 ( 1440) hydrogen bonds : angle 5.54818 ( 4197) covalent geometry : bond 0.00337 (25142) covalent geometry : angle 0.63738 (34089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1533 LEU cc_start: 0.8226 (tp) cc_final: 0.7984 (tp) REVERT: A 2222 MET cc_start: 0.8077 (mpp) cc_final: 0.7846 (mtm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3709 time to fit residues: 212.3059 Evaluate side-chains 262 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1559 HIS A1566 GLN A2187 GLN A2377 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2588 HIS ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3650 ASN A4063 ASN A4466 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.156226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115819 restraints weight = 45318.035| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.85 r_work: 0.3450 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25142 Z= 0.136 Angle : 0.568 7.746 34089 Z= 0.284 Chirality : 0.041 0.229 3821 Planarity : 0.004 0.055 4367 Dihedral : 5.822 74.592 3377 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 0.85 % Allowed : 6.54 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.86 (0.16), residues: 3035 helix: 2.07 (0.12), residues: 1760 sheet: -0.60 (0.37), residues: 215 loop : 0.32 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2825 HIS 0.005 0.001 HIS A4119 PHE 0.021 0.002 PHE A3529 TYR 0.014 0.001 TYR A3836 ARG 0.006 0.001 ARG A2610 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 1440) hydrogen bonds : angle 4.43845 ( 4197) covalent geometry : bond 0.00309 (25142) covalent geometry : angle 0.56799 (34089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1533 LEU cc_start: 0.7874 (tp) cc_final: 0.7661 (tp) REVERT: A 1564 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 1814 GLU cc_start: 0.8272 (tp30) cc_final: 0.8060 (tp30) REVERT: A 1842 MET cc_start: 0.8826 (ttm) cc_final: 0.8518 (tpp) REVERT: A 2055 TYR cc_start: 0.8898 (t80) cc_final: 0.8623 (t80) REVERT: A 2614 ASP cc_start: 0.7193 (m-30) cc_final: 0.6933 (t0) REVERT: A 2643 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7725 (tpp80) REVERT: A 2779 MET cc_start: 0.8250 (mtm) cc_final: 0.7733 (tpt) REVERT: A 3108 GLU cc_start: 0.8272 (tp30) cc_final: 0.7969 (tp30) REVERT: A 3153 THR cc_start: 0.8198 (t) cc_final: 0.7914 (p) REVERT: A 3664 LEU cc_start: 0.8230 (mp) cc_final: 0.8012 (tt) REVERT: A 3856 LEU cc_start: 0.8283 (tp) cc_final: 0.8083 (tt) REVERT: A 4281 GLU cc_start: 0.8305 (pm20) cc_final: 0.8096 (pp20) outliers start: 23 outliers final: 15 residues processed: 324 average time/residue: 0.3381 time to fit residues: 177.4995 Evaluate side-chains 269 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4516 VAL 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: 71.395 > 50: distance: 44 - 47: 33.473 distance: 47 - 53: 57.713 distance: 48 - 49: 68.843 distance: 48 - 51: 39.854 distance: 49 - 50: 57.162 distance: 49 - 54: 69.814 distance: 51 - 52: 56.926 distance: 52 - 53: 40.870 distance: 54 - 55: 34.358 distance: 55 - 56: 55.983 distance: 55 - 58: 40.747 distance: 56 - 57: 41.061 distance: 56 - 62: 41.290 distance: 58 - 59: 56.885 distance: 59 - 60: 50.946 distance: 59 - 61: 46.344 distance: 62 - 63: 41.279 distance: 63 - 64: 39.341 distance: 64 - 65: 46.424 distance: 64 - 66: 40.660 distance: 66 - 67: 56.335 distance: 67 - 68: 56.731 distance: 67 - 70: 40.308 distance: 68 - 69: 56.591 distance: 68 - 80: 55.407 distance: 70 - 71: 39.451 distance: 71 - 72: 60.303 distance: 71 - 73: 45.230 distance: 72 - 74: 44.100 distance: 73 - 75: 60.520 distance: 73 - 76: 22.565 distance: 74 - 75: 57.974 distance: 75 - 77: 38.899 distance: 76 - 78: 40.701 distance: 77 - 79: 3.867 distance: 78 - 79: 55.291 distance: 81 - 82: 39.180 distance: 81 - 84: 56.468 distance: 82 - 83: 56.091 distance: 82 - 86: 38.710 distance: 84 - 85: 70.048 distance: 86 - 87: 41.173 distance: 87 - 88: 69.035 distance: 87 - 90: 67.988 distance: 88 - 89: 57.330 distance: 88 - 95: 68.003 distance: 90 - 91: 41.240 distance: 91 - 92: 41.875 distance: 92 - 93: 9.434 distance: 93 - 94: 60.959 distance: 95 - 96: 54.721 distance: 96 - 97: 57.058 distance: 96 - 99: 39.452 distance: 97 - 98: 57.566 distance: 97 - 104: 40.800 distance: 99 - 100: 56.338 distance: 100 - 101: 39.175 distance: 101 - 102: 32.793 distance: 102 - 103: 58.265 distance: 104 - 105: 7.928 distance: 105 - 106: 69.075 distance: 105 - 108: 40.536 distance: 106 - 116: 55.587 distance: 108 - 109: 56.079 distance: 109 - 110: 38.907 distance: 110 - 112: 57.028 distance: 111 - 113: 39.496 distance: 113 - 114: 54.483 distance: 114 - 115: 57.408 distance: 116 - 117: 70.404 distance: 117 - 118: 42.917 distance: 117 - 120: 41.316 distance: 118 - 119: 45.461 distance: 118 - 125: 58.942 distance: 120 - 121: 35.486 distance: 121 - 122: 59.774 distance: 122 - 123: 40.281 distance: 122 - 124: 38.952 distance: 125 - 126: 40.209 distance: 126 - 127: 38.861 distance: 126 - 129: 62.100 distance: 127 - 128: 39.916 distance: 127 - 136: 34.843 distance: 129 - 130: 42.168 distance: 130 - 131: 64.502 distance: 130 - 132: 55.682 distance: 131 - 133: 43.006 distance: 132 - 134: 43.063 distance: 133 - 135: 65.100 distance: 134 - 135: 44.327