Starting phenix.real_space_refine on Wed Jan 14 04:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzf_41757/01_2026/8tzf_41757.map" } resolution = 3.4 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= 0.020 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 2 5.49 5 S 57 5.16 5 C 7737 2.51 5 N 2128 2.21 5 O 2243 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 11685 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 69, 'TRANS': 1519} Chain breaks: 28 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1023 Unresolved non-hydrogen angles: 1294 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'ASP:plan': 22, 'HIS:plan': 9, 'GLN:plan1': 15, 'TYR:plan': 9, 'GLU:plan': 19, 'ARG:plan': 13, 'PHE:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 540 Chain: "B" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 4, 'HIS:plan': 7, 'GLU:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.71, per 1000 atoms: 0.22 Number of scatterers: 12170 At special positions: 0 Unit cell: (104.5, 109.25, 151.05, 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 57 16.00 P 2 15.00 F 3 9.00 O 2243 8.00 N 2128 7.00 C 7737 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: 1.10 Conformation dependent library (CDL) restraints added in 612.7 milliseconds 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 18 sheets defined 37.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 611 removed outlier: 3.794A pdb=" N GLY A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 638 removed outlier: 4.020A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 655 removed outlier: 4.298A pdb=" N GLY A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.911A pdb=" N VAL A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 703 Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.737A pdb=" N ASP A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.530A pdb=" N GLN A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.564A pdb=" N VAL A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.503A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 835 through 849 Processing helix chain 'A' and resid 997 through 1002 removed outlier: 4.161A pdb=" N GLN A1002 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1012 removed outlier: 3.733A pdb=" N GLU A1011 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A1012 " --> pdb=" O HIS A1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1012' Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 4.204A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.783A pdb=" N VAL A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 3.522A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 removed outlier: 3.651A pdb=" N LEU A1267 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1328 Processing helix chain 'A' and resid 1346 through 1356 removed outlier: 3.527A pdb=" N LYS A1356 " --> pdb=" O GLN A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.550A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1429 No H-bonds generated for 'chain 'A' and resid 1427 through 1429' Processing helix chain 'A' and resid 1430 through 1442 removed outlier: 4.639A pdb=" N TRP A1434 " --> pdb=" O ALA A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1464 removed outlier: 3.595A pdb=" N ARG A1462 " --> pdb=" O ASP A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1473 removed outlier: 3.616A pdb=" N LYS A1468 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A1470 " --> pdb=" O MET A1466 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1550 through 1560 Processing helix chain 'A' and resid 1567 through 1580 removed outlier: 4.700A pdb=" N HIS A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.662A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1654 removed outlier: 4.540A pdb=" N LYS A1651 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1652 " --> pdb=" O GLN A1648 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1653 " --> pdb=" O TYR A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1710 removed outlier: 3.567A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1828 through 1835 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1915 through 1925 removed outlier: 3.789A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A1924 " --> pdb=" O GLU A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 Processing helix chain 'A' and resid 1967 through 1988 removed outlier: 4.004A pdb=" N HIS A1972 " --> pdb=" O ARG A1968 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG A1973 " --> pdb=" O THR A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 2051 through 2068 removed outlier: 3.630A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.715A pdb=" N GLU A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2124 through 2133 removed outlier: 3.583A pdb=" N PHE A2129 " --> pdb=" O SER A2125 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A2130 " --> pdb=" O ALA A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.657A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2341 No H-bonds generated for 'chain 'A' and resid 2339 through 2341' Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2396 Processing helix chain 'A' and resid 2499 through 2521 removed outlier: 3.908A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A2507 " --> pdb=" O GLU A2503 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A2517 " --> pdb=" O VAL A2513 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 150 through 159 removed outlier: 4.060A pdb=" N LEU B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.513A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.965A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 7.320A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA5, first strand: chain 'A' and resid 1373 through 1376 removed outlier: 6.810A pdb=" N MET A1335 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TRP A1393 " --> pdb=" O MET A1335 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A1337 " --> pdb=" O TRP A1393 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1417 through 1418 removed outlier: 6.274A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 removed outlier: 3.938A pdb=" N ILE A1548 " --> pdb=" O TYR A1596 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A1596 " --> pdb=" O ILE A1548 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1690 through 1694 removed outlier: 6.910A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 3.603A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.661A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2155 through 2158 Processing sheet with id=AB5, first strand: chain 'A' and resid 2215 through 2219 removed outlier: 4.331A pdb=" N THR A2219 " --> pdb=" O THR A2223 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR A2223 " --> pdb=" O THR A2219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2248 through 2249 removed outlier: 3.581A pdb=" N TYR A2249 " --> pdb=" O LEU A2264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2303 through 2304 removed outlier: 3.922A pdb=" N SER A2304 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP A2316 " --> pdb=" O SER A2304 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A2317 " --> pdb=" O PHE A2324 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A2325 " --> pdb=" O LYS A2334 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2358 removed outlier: 6.787A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2418 removed outlier: 3.520A pdb=" N THR A2416 " --> pdb=" O GLY A2428 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1218 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: 2.71 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2065 1.30 - 1.43: 2907 1.43 - 1.56: 7295 1.56 - 1.68: 6 1.68 - 1.81: 85 Bond restraints: 12358 Sorted by residual: bond pdb=" C19 T3X A2602 " pdb=" N18 T3X A2602 " ideal model delta sigma weight residual 1.466 1.312 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C22 T3X A2602 " pdb=" N21 T3X A2602 " ideal model delta sigma weight residual 1.467 1.314 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C23 T3X A2602 " pdb=" N18 T3X A2602 " ideal model delta sigma weight residual 1.456 1.304 0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C24 T3X A2602 " pdb=" N21 T3X A2602 " ideal model delta sigma weight residual 1.451 1.301 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C20 T3X A2602 " pdb=" N21 T3X A2602 " ideal model delta sigma weight residual 1.456 1.317 0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 12353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 16581 2.34 - 4.68: 176 4.68 - 7.02: 27 7.02 - 9.36: 8 9.36 - 11.70: 4 Bond angle restraints: 16796 Sorted by residual: angle pdb=" CA PRO A1262 " pdb=" N PRO A1262 " pdb=" CD PRO A1262 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" CA PRO A1377 " pdb=" N PRO A1377 " pdb=" CD PRO A1377 " ideal model delta sigma weight residual 112.00 104.97 7.03 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C33 T3X A2602 " pdb=" C37 T3X A2602 " pdb=" N36 T3X A2602 " ideal model delta sigma weight residual 110.71 122.41 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N ALA A1589 " pdb=" CA ALA A1589 " pdb=" C ALA A1589 " ideal model delta sigma weight residual 114.04 109.42 4.62 1.24e+00 6.50e-01 1.39e+01 angle pdb=" C37 T3X A2602 " pdb=" N36 T3X A2602 " pdb=" N35 T3X A2602 " ideal model delta sigma weight residual 106.89 95.88 11.01 3.00e+00 1.11e-01 1.35e+01 ... (remaining 16791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.36: 6559 20.36 - 40.72: 743 40.72 - 61.08: 150 61.08 - 81.44: 31 81.44 - 101.80: 5 Dihedral angle restraints: 7488 sinusoidal: 2624 harmonic: 4864 Sorted by residual: dihedral pdb=" CA TYR A1419 " pdb=" C TYR A1419 " pdb=" N ASP A1420 " pdb=" CA ASP A1420 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C03 T3X A2602 " pdb=" C29 T3X A2602 " pdb=" C30 T3X A2602 " pdb=" C31 T3X A2602 " ideal model delta sinusoidal sigma weight residual -52.76 49.04 -101.80 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" CA VAL A1065 " pdb=" C VAL A1065 " pdb=" N SER A1066 " pdb=" CA SER A1066 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 7485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1338 0.037 - 0.075: 478 0.075 - 0.112: 167 0.112 - 0.150: 30 0.150 - 0.187: 1 Chirality restraints: 2014 Sorted by residual: chirality pdb=" CG LEU A1553 " pdb=" CB LEU A1553 " pdb=" CD1 LEU A1553 " pdb=" CD2 LEU A1553 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA LEU A1569 " pdb=" N LEU A1569 " pdb=" C LEU A1569 " pdb=" CB LEU A1569 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CG LEU A1914 " pdb=" CB LEU A1914 " pdb=" CD1 LEU A1914 " pdb=" CD2 LEU A1914 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2011 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1188 " -0.046 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO A1189 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A1189 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1189 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1261 " -0.047 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO A1262 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1262 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1262 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1782 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" CG ASP A1782 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A1782 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A1782 " 0.014 2.00e-02 2.50e+03 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 180 2.66 - 3.22: 11377 3.22 - 3.78: 17934 3.78 - 4.34: 23367 4.34 - 4.90: 39305 Nonbonded interactions: 92163 Sorted by model distance: nonbonded pdb=" OG SER A1345 " pdb=" O TYR A1419 " model vdw 2.099 3.040 nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.188 3.040 nonbonded pdb=" O SER A 990 " pdb=" ND2 ASN A1021 " model vdw 2.195 3.120 nonbonded pdb=" O GLY A1886 " pdb=" OG SER A1889 " model vdw 2.195 3.040 nonbonded pdb=" O SER A2341 " pdb=" OG SER A2341 " model vdw 2.227 3.040 ... (remaining 92158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.170 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.350 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.006 0.154 12358 Z= 0.259 Angle : 0.646 11.701 16796 Z= 0.318 Chirality : 0.043 0.187 2014 Planarity : 0.005 0.071 2150 Dihedral : 17.873 101.801 4298 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.61 % Allowed : 34.73 % Favored : 64.66 % 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 are not related in a simple way. whole: -0.85 (0.22), residues: 1607 helix: 1.15 (0.23), residues: 574 sheet: -1.40 (0.33), residues: 258 loop : -1.60 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1707 TYR 0.019 0.001 TYR A1419 PHE 0.020 0.001 PHE A1170 TRP 0.021 0.002 TRP A1376 HIS 0.004 0.001 HIS A1972 Details of bonding type rmsd covalent geometry : bond 0.00581 (12358) covalent geometry : angle 0.64604 (16796) hydrogen bonds : bond 0.14704 ( 429) hydrogen bonds : angle 6.05257 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.470 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 138 average time/residue: 0.1084 time to fit residues: 21.9484 Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1871 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1577 ASN A1999 ASN A2499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127133 restraints weight = 19365.209| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.15 r_work: 0.3437 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12358 Z= 0.122 Angle : 0.537 8.956 16796 Z= 0.269 Chirality : 0.042 0.136 2014 Planarity : 0.004 0.067 2150 Dihedral : 5.112 47.344 1773 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.49 % Allowed : 32.02 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1607 helix: 1.20 (0.23), residues: 585 sheet: -1.46 (0.33), residues: 258 loop : -1.54 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1957 TYR 0.012 0.001 TYR A1733 PHE 0.012 0.001 PHE A1170 TRP 0.010 0.001 TRP A2426 HIS 0.005 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00296 (12358) covalent geometry : angle 0.53705 (16796) hydrogen bonds : bond 0.03011 ( 429) hydrogen bonds : angle 4.76041 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.532 Fit side-chains REVERT: A 1458 ASP cc_start: 0.8087 (m-30) cc_final: 0.7716 (p0) REVERT: A 1689 GLU cc_start: 0.8331 (pm20) cc_final: 0.7938 (pm20) REVERT: A 1944 MET cc_start: 0.7617 (ptp) cc_final: 0.7390 (ptm) REVERT: A 2018 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.6979 (m-80) outliers start: 40 outliers final: 14 residues processed: 176 average time/residue: 0.1077 time to fit residues: 28.2230 Evaluate side-chains 143 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1577 ASN Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1758 HIS Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2132 LEU Chi-restraints excluded: chain A residue 2136 GLU Chi-restraints excluded: chain A residue 2152 VAL Chi-restraints excluded: chain A residue 2511 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.46 > 50: distance: 18 - 47: 9.838 distance: 34 - 39: 3.427 distance: 39 - 40: 6.196 distance: 40 - 41: 7.189 distance: 40 - 43: 3.108 distance: 41 - 42: 5.019 distance: 41 - 47: 4.749 distance: 42 - 77: 21.979 distance: 43 - 44: 5.490 distance: 44 - 45: 3.789 distance: 44 - 46: 5.063 distance: 47 - 48: 7.531 distance: 48 - 49: 8.516 distance: 48 - 51: 3.947 distance: 49 - 50: 5.670 distance: 49 - 56: 8.476 distance: 50 - 85: 11.724 distance: 51 - 52: 7.225 distance: 52 - 53: 10.735 distance: 53 - 54: 5.235 distance: 53 - 55: 11.432 distance: 56 - 57: 4.650 distance: 57 - 58: 10.417 distance: 57 - 60: 8.641 distance: 58 - 59: 22.651 distance: 58 - 66: 29.217 distance: 59 - 90: 19.983 distance: 60 - 61: 6.578 distance: 61 - 62: 16.744 distance: 61 - 63: 20.366 distance: 62 - 64: 10.219 distance: 63 - 65: 8.840 distance: 64 - 65: 21.878 distance: 66 - 67: 13.248 distance: 67 - 68: 6.159 distance: 67 - 70: 13.629 distance: 68 - 69: 4.200 distance: 68 - 77: 12.941 distance: 69 - 98: 31.715 distance: 70 - 71: 13.716 distance: 71 - 72: 24.862 distance: 72 - 73: 7.911 distance: 73 - 74: 16.373 distance: 74 - 75: 5.059 distance: 74 - 76: 16.157 distance: 77 - 78: 10.780 distance: 78 - 79: 20.253 distance: 78 - 81: 17.953 distance: 79 - 80: 13.346 distance: 79 - 85: 17.904 distance: 80 - 108: 24.312 distance: 81 - 82: 5.890 distance: 81 - 83: 10.477 distance: 82 - 84: 12.334 distance: 85 - 86: 17.578 distance: 86 - 87: 3.005 distance: 86 - 89: 6.845 distance: 87 - 88: 4.513 distance: 87 - 90: 4.307 distance: 88 - 115: 11.983 distance: 90 - 91: 4.685 distance: 91 - 92: 10.862 distance: 91 - 94: 6.113 distance: 92 - 93: 13.798 distance: 92 - 98: 7.202 distance: 93 - 120: 11.633 distance: 94 - 95: 20.599 distance: 95 - 96: 39.384 distance: 95 - 97: 17.624 distance: 98 - 99: 11.385 distance: 99 - 102: 14.984 distance: 100 - 108: 4.713 distance: 101 - 127: 22.400 distance: 102 - 103: 7.768 distance: 103 - 105: 6.454 distance: 104 - 106: 6.168 distance: 105 - 107: 11.642 distance: 106 - 107: 7.172 distance: 108 - 109: 12.849 distance: 109 - 110: 17.259 distance: 109 - 112: 4.576 distance: 110 - 111: 6.371 distance: 110 - 115: 6.947 distance: 111 - 131: 14.969 distance: 112 - 113: 25.555 distance: 112 - 114: 38.420 distance: 115 - 116: 6.812 distance: 116 - 117: 19.943 distance: 116 - 119: 14.344 distance: 117 - 118: 5.161 distance: 117 - 120: 10.151 distance: 118 - 139: 9.040