Starting phenix.real_space_refine on Fri Jul 3 09:53:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473.map" model { file = "/net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x28_66473/07_2026/9x28_66473_neut.cif" } resolution = 2.83 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= 0.005 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8362 2.51 5 N 2217 2.21 5 O 2365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13020 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1657, 13020 Classifications: {'peptide': 1657} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 88, 'TRANS': 1568} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.87, per 1000 atoms: 0.22 Number of scatterers: 13020 At special positions: 0 Unit cell: (92.71, 110.23, 144.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2365 8.00 N 2217 7.00 C 8362 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: 1.01 Conformation dependent library (CDL) restraints added in 602.8 milliseconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 59.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.705A pdb=" N LEU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.609A pdb=" N TRP A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.742A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 106' Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.992A pdb=" N ARG A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 203 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 249 removed outlier: 4.626A pdb=" N PHE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.948A pdb=" N PHE A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 290 removed outlier: 4.152A pdb=" N VAL A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 318 through 346 Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.853A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.574A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.977A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 465 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 513 through 516 Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.780A pdb=" N PHE A 558 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 627 through 646 removed outlier: 3.925A pdb=" N ILE A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 688 Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 738 through 756 Processing helix chain 'A' and resid 761 through 779 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.643A pdb=" N ILE A 784 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 805 through 813 Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.471A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.558A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 877 through 889 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 903 through 916 Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.792A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 957 Processing helix chain 'A' and resid 962 through 979 Processing helix chain 'A' and resid 986 through 991 removed outlier: 4.015A pdb=" N GLU A 991 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1081 through 1100 removed outlier: 3.603A pdb=" N ARG A1100 " --> pdb=" O TRP A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1118 Processing helix chain 'A' and resid 1151 through 1157 removed outlier: 3.639A pdb=" N TRP A1157 " --> pdb=" O ILE A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1196 Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'A' and resid 1255 through 1277 removed outlier: 3.504A pdb=" N SER A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1295 removed outlier: 3.959A pdb=" N ARG A1294 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A1295 " --> pdb=" O LEU A1292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1291 through 1295' Processing helix chain 'A' and resid 1296 through 1303 Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 4.001A pdb=" N VAL A1308 " --> pdb=" O PRO A1304 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1335 Processing helix chain 'A' and resid 1338 through 1348 Processing helix chain 'A' and resid 1350 through 1356 Processing helix chain 'A' and resid 1359 through 1367 Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1371 through 1382 removed outlier: 3.588A pdb=" N LEU A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1385 No H-bonds generated for 'chain 'A' and resid 1383 through 1385' Processing helix chain 'A' and resid 1386 through 1395 Processing helix chain 'A' and resid 1396 through 1397 No H-bonds generated for 'chain 'A' and resid 1396 through 1397' Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.900A pdb=" N TYR A1401 " --> pdb=" O ASN A1398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A1403 " --> pdb=" O LYS A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1407 No H-bonds generated for 'chain 'A' and resid 1405 through 1407' Processing helix chain 'A' and resid 1408 through 1416 removed outlier: 3.500A pdb=" N ALA A1414 " --> pdb=" O ASP A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1465 removed outlier: 4.080A pdb=" N ASN A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN A1453 " --> pdb=" O LYS A1449 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1464 " --> pdb=" O VAL A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1485 Processing helix chain 'A' and resid 1499 through 1509 Processing helix chain 'A' and resid 1512 through 1517 Processing helix chain 'A' and resid 1519 through 1525 Processing helix chain 'A' and resid 1589 through 1594 removed outlier: 3.779A pdb=" N ILE A1593 " --> pdb=" O LEU A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1616 Processing helix chain 'A' and resid 1622 through 1641 Processing helix chain 'A' and resid 1681 through 1687 removed outlier: 3.542A pdb=" N ALA A1685 " --> pdb=" O CYS A1681 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1686 " --> pdb=" O PRO A1682 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1681 through 1687' Processing helix chain 'A' and resid 1692 through 1698 Processing helix chain 'A' and resid 1701 through 1709 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.503A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 493 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 655 Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 707 Processing sheet with id=AA7, first strand: chain 'A' and resid 1022 through 1026 Processing sheet with id=AA8, first strand: chain 'A' and resid 1432 through 1434 removed outlier: 4.073A pdb=" N ASP A1432 " --> pdb=" O LEU A1580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1492 through 1493 removed outlier: 3.548A pdb=" N ILE A1471 " --> pdb=" O ILE A1492 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A1470 " --> pdb=" O VAL A1534 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A1533 " --> pdb=" O ILE A1543 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU A1545 " --> pdb=" O ALA A1533 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1658 through 1662 687 hydrogen bonds defined for protein. 1929 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: 2.77 Time building geometry restraints manager: 1.35 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: 3932 1.34 - 1.46: 1941 1.46 - 1.57: 7334 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 13318 Sorted by residual: bond pdb=" N VAL A1456 " pdb=" CA VAL A1456 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.02e+00 bond pdb=" N VAL A1461 " pdb=" CA VAL A1461 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.34e+00 bond pdb=" N VAL A1460 " pdb=" CA VAL A1460 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.26e+00 bond pdb=" N MET A1459 " pdb=" CA MET A1459 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.46e+00 bond pdb=" N ARG A 58 " pdb=" CA ARG A 58 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.23e-02 6.61e+03 5.38e+00 ... (remaining 13313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 17807 1.68 - 3.37: 242 3.37 - 5.05: 37 5.05 - 6.74: 18 6.74 - 8.42: 6 Bond angle restraints: 18110 Sorted by residual: angle pdb=" C VAL A1611 " pdb=" N MET A1612 " pdb=" CA MET A1612 " ideal model delta sigma weight residual 121.14 114.61 6.53 1.75e+00 3.27e-01 1.39e+01 angle pdb=" CA MET A1612 " pdb=" CB MET A1612 " pdb=" CG MET A1612 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CB ARG A 880 " pdb=" CG ARG A 880 " pdb=" CD ARG A 880 " ideal model delta sigma weight residual 111.30 118.03 -6.73 2.30e+00 1.89e-01 8.56e+00 angle pdb=" CA MET A1459 " pdb=" C MET A1459 " pdb=" O MET A1459 " ideal model delta sigma weight residual 120.82 117.89 2.93 1.05e+00 9.07e-01 7.77e+00 angle pdb=" CA TRP A 638 " pdb=" CB TRP A 638 " pdb=" CG TRP A 638 " ideal model delta sigma weight residual 113.60 118.82 -5.22 1.90e+00 2.77e-01 7.54e+00 ... (remaining 18105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7019 17.97 - 35.95: 777 35.95 - 53.92: 174 53.92 - 71.89: 35 71.89 - 89.87: 10 Dihedral angle restraints: 8015 sinusoidal: 3165 harmonic: 4850 Sorted by residual: dihedral pdb=" CA ASP A 924 " pdb=" CB ASP A 924 " pdb=" CG ASP A 924 " pdb=" OD1 ASP A 924 " ideal model delta sinusoidal sigma weight residual -30.00 -89.61 59.61 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " pdb=" OD1 ASP A 358 " ideal model delta sinusoidal sigma weight residual -30.00 -86.74 56.74 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CG ARG A 464 " pdb=" CD ARG A 464 " pdb=" NE ARG A 464 " pdb=" CZ ARG A 464 " ideal model delta sinusoidal sigma weight residual 90.00 134.80 -44.80 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 8012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1477 0.035 - 0.070: 415 0.070 - 0.105: 144 0.105 - 0.139: 51 0.139 - 0.174: 4 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA MET A1459 " pdb=" N MET A1459 " pdb=" C MET A1459 " pdb=" CB MET A1459 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA VAL A1456 " pdb=" N VAL A1456 " pdb=" C VAL A1456 " pdb=" CB VAL A1456 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA VAL A1461 " pdb=" N VAL A1461 " pdb=" C VAL A1461 " pdb=" CB VAL A1461 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2088 not shown) Planarity restraints: 2294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1486 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A1487 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A1487 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1487 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 901 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 902 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 638 " -0.014 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP A 638 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 638 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 638 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 638 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 638 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 638 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 638 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 638 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 638 " -0.000 2.00e-02 2.50e+03 ... (remaining 2291 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1722 2.76 - 3.29: 12514 3.29 - 3.83: 22541 3.83 - 4.36: 24427 4.36 - 4.90: 43055 Nonbonded interactions: 104259 Sorted by model distance: nonbonded pdb=" O ASP A 913 " pdb=" OG1 THR A 916 " model vdw 2.222 3.040 nonbonded pdb=" N GLU A 432 " pdb=" OE1 GLU A 432 " model vdw 2.261 3.120 nonbonded pdb=" N GLU A1234 " pdb=" OE1 GLU A1234 " model vdw 2.265 3.120 nonbonded pdb=" OD2 ASP A 819 " pdb=" NH2 ARG A1002 " model vdw 2.286 3.120 nonbonded pdb=" O MET A 917 " pdb=" NH2 ARG A1008 " model vdw 2.302 3.120 ... (remaining 104254 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.500 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.002 0.036 13318 Z= 0.121 Angle : 0.512 8.423 18110 Z= 0.262 Chirality : 0.040 0.174 2091 Planarity : 0.004 0.086 2294 Dihedral : 15.820 89.868 4877 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.28 % Allowed : 21.92 % Favored : 77.80 % 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: 1.53 (0.22), residues: 1645 helix: 2.25 (0.19), residues: 829 sheet: 0.75 (0.58), residues: 86 loop : -0.41 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 880 TYR 0.013 0.001 TYR A1097 PHE 0.016 0.001 PHE A1343 TRP 0.030 0.001 TRP A 638 HIS 0.004 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (13318) covalent geometry : angle 0.51223 / 0.26 (18110) hydrogen bonds : bond 0.12509 / 8.60 ( 687) hydrogen bonds : angle 4.69602 / 3.45 ( 1929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 308 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8043 (mt) cc_final: 0.7503 (mt) REVERT: A 393 ASP cc_start: 0.7601 (t0) cc_final: 0.7041 (p0) REVERT: A 778 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7422 (tp30) REVERT: A 1267 LEU cc_start: 0.9584 (tp) cc_final: 0.9377 (mm) REVERT: A 1332 MET cc_start: 0.7932 (ttm) cc_final: 0.7670 (ttp) REVERT: A 1401 TYR cc_start: 0.8306 (m-80) cc_final: 0.8091 (m-10) REVERT: A 1459 MET cc_start: 0.9087 (mmt) cc_final: 0.8845 (mmt) REVERT: A 1604 LEU cc_start: 0.9211 (mt) cc_final: 0.8985 (mp) REVERT: A 1608 TYR cc_start: 0.8699 (t80) cc_final: 0.8335 (t80) outliers start: 4 outliers final: 1 residues processed: 310 average time/residue: 0.5049 time to fit residues: 173.3495 Evaluate side-chains 181 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1272 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 556 ASN A1166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090956 restraints weight = 24763.572| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.37 r_work: 0.3139 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13318 Z= 0.175 Angle : 0.618 8.513 18110 Z= 0.310 Chirality : 0.044 0.188 2091 Planarity : 0.004 0.055 2294 Dihedral : 3.827 47.681 1810 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.97 % Allowed : 22.89 % Favored : 73.14 % 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: 1.35 (0.21), residues: 1645 helix: 2.03 (0.18), residues: 839 sheet: 0.58 (0.52), residues: 106 loop : -0.43 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1310 TYR 0.020 0.001 TYR A1035 PHE 0.018 0.002 PHE A1341 TRP 0.023 0.001 TRP A 638 HIS 0.011 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (13318) covalent geometry : angle 0.61821 / 0.31 (18110) hydrogen bonds : bond 0.03615 / 2.45 ( 687) hydrogen bonds : angle 4.21124 / 3.14 ( 1929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 42 SER cc_start: 0.2522 (OUTLIER) cc_final: 0.1893 (m) REVERT: A 393 ASP cc_start: 0.8382 (t0) cc_final: 0.7323 (p0) REVERT: A 488 ARG cc_start: 0.7547 (mtp85) cc_final: 0.6987 (mmt180) REVERT: A 511 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 521 MET cc_start: 0.8351 (tpt) cc_final: 0.8093 (tpt) REVERT: A 622 MET cc_start: 0.7272 (tpt) cc_final: 0.7025 (tpp) REVERT: A 647 ASN cc_start: 0.8557 (t0) cc_final: 0.8280 (m-40) REVERT: A 778 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8226 (tp30) REVERT: A 962 VAL cc_start: 0.8575 (t) cc_final: 0.8369 (t) REVERT: A 1039 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 1341 PHE cc_start: 0.8472 (t80) cc_final: 0.8232 (t80) REVERT: A 1354 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8584 (pp) REVERT: A 1370 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.5464 (t-170) REVERT: A 1374 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 1393 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 1604 LEU cc_start: 0.9379 (mt) cc_final: 0.9073 (mt) REVERT: A 1608 TYR cc_start: 0.9019 (t80) cc_final: 0.8808 (t80) outliers start: 57 outliers final: 16 residues processed: 240 average time/residue: 0.4781 time to fit residues: 128.2907 Evaluate side-chains 195 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1263 CYS Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1393 GLU Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1593 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.0470 chunk 127 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 199 GLN A 548 ASN A1025 HIS A1323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078533 restraints weight = 24898.051| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.36 r_work: 0.2929 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 13318 Z= 0.320 Angle : 0.724 14.187 18110 Z= 0.361 Chirality : 0.048 0.235 2091 Planarity : 0.005 0.044 2294 Dihedral : 4.339 44.529 1810 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.29 % Allowed : 22.20 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1645 helix: 1.66 (0.18), residues: 841 sheet: 0.19 (0.48), residues: 115 loop : -0.61 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1504 TYR 0.023 0.002 TYR A1164 PHE 0.028 0.002 PHE A 230 TRP 0.020 0.002 TRP A 638 HIS 0.010 0.002 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.32 (13318) covalent geometry : angle 0.72422 / 0.36 (18110) hydrogen bonds : bond 0.04471 / 3.11 ( 687) hydrogen bonds : angle 4.43337 / 3.30 ( 1929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 153 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.2133 (OUTLIER) cc_final: 0.1591 (m) REVERT: A 58 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7144 (tmt90) REVERT: A 168 ASP cc_start: 0.8893 (m-30) cc_final: 0.8672 (t0) REVERT: A 387 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7663 (mm) REVERT: A 393 ASP cc_start: 0.8697 (t0) cc_final: 0.7427 (p0) REVERT: A 482 GLU cc_start: 0.9288 (tp30) cc_final: 0.9058 (tp30) REVERT: A 488 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7094 (mmt180) REVERT: A 511 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7714 (tp30) REVERT: A 521 MET cc_start: 0.8353 (tpt) cc_final: 0.7717 (tpt) REVERT: A 622 MET cc_start: 0.8149 (tpt) cc_final: 0.7801 (tpp) REVERT: A 626 MET cc_start: 0.6696 (ppp) cc_final: 0.6374 (ppp) REVERT: A 647 ASN cc_start: 0.8659 (t0) cc_final: 0.8294 (m-40) REVERT: A 778 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8247 (tp30) REVERT: A 891 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8313 (p90) REVERT: A 1039 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 1068 VAL cc_start: 0.4623 (OUTLIER) cc_final: 0.4373 (p) REVERT: A 1089 ASP cc_start: 0.9210 (m-30) cc_final: 0.8979 (m-30) REVERT: A 1257 CYS cc_start: 0.8679 (m) cc_final: 0.8221 (p) REVERT: A 1332 MET cc_start: 0.7960 (ttp) cc_final: 0.7691 (ttm) REVERT: A 1341 PHE cc_start: 0.8655 (t80) cc_final: 0.8415 (t80) REVERT: A 1370 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.5575 (t-170) REVERT: A 1393 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 1459 MET cc_start: 0.9443 (mmt) cc_final: 0.8709 (tpp) REVERT: A 1486 LEU cc_start: 0.9242 (mp) cc_final: 0.8962 (tm) REVERT: A 1604 LEU cc_start: 0.9391 (mt) cc_final: 0.9133 (mt) outliers start: 76 outliers final: 23 residues processed: 215 average time/residue: 0.4964 time to fit residues: 119.2862 Evaluate side-chains 171 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1393 GLU Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain A residue 1593 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3613 > 50: distance: 29 - 54: 29.572 distance: 40 - 62: 22.938 distance: 46 - 70: 18.676 distance: 50 - 54: 27.472 distance: 54 - 55: 39.840 distance: 55 - 56: 18.840 distance: 55 - 58: 33.373 distance: 56 - 57: 25.702 distance: 56 - 62: 22.244 distance: 58 - 59: 23.377 distance: 59 - 60: 17.303 distance: 59 - 61: 24.394 distance: 62 - 63: 30.223 distance: 63 - 64: 35.843 distance: 63 - 66: 26.400 distance: 64 - 65: 28.312 distance: 64 - 70: 29.569 distance: 66 - 67: 24.965 distance: 66 - 68: 30.026 distance: 67 - 69: 24.392 distance: 70 - 71: 32.130 distance: 71 - 72: 31.680 distance: 71 - 74: 52.973 distance: 72 - 73: 27.876 distance: 72 - 78: 29.694 distance: 74 - 75: 11.625 distance: 75 - 76: 23.258 distance: 76 - 77: 16.148 distance: 78 - 79: 17.117 distance: 79 - 80: 23.354 distance: 79 - 82: 43.724 distance: 80 - 81: 38.045 distance: 80 - 86: 35.380 distance: 82 - 83: 38.785 distance: 82 - 84: 31.486 distance: 83 - 85: 5.181 distance: 86 - 87: 4.901 distance: 87 - 88: 11.395 distance: 87 - 90: 20.412 distance: 88 - 89: 20.552 distance: 88 - 97: 10.508 distance: 90 - 91: 20.497 distance: 91 - 92: 15.553 distance: 93 - 94: 3.247 distance: 94 - 96: 3.393 distance: 97 - 98: 18.691 distance: 98 - 99: 23.655 distance: 99 - 100: 18.055 distance: 99 - 101: 21.977 distance: 101 - 102: 19.942 distance: 102 - 103: 22.071 distance: 102 - 105: 27.461 distance: 103 - 104: 13.900 distance: 103 - 109: 8.575 distance: 105 - 106: 21.806 distance: 106 - 107: 13.335 distance: 106 - 108: 18.304 distance: 109 - 110: 18.753 distance: 110 - 111: 7.974 distance: 110 - 113: 29.623 distance: 111 - 112: 13.866 distance: 111 - 117: 19.855 distance: 113 - 114: 18.862 distance: 114 - 115: 12.907 distance: 114 - 116: 10.275 distance: 117 - 118: 33.256 distance: 118 - 119: 20.168 distance: 118 - 121: 17.081 distance: 119 - 120: 34.520 distance: 119 - 125: 29.210 distance: 120 - 153: 17.300 distance: 121 - 122: 58.196 distance: 121 - 123: 34.022 distance: 122 - 124: 34.785 distance: 125 - 126: 36.065 distance: 126 - 127: 39.601 distance: 126 - 129: 19.436 distance: 127 - 128: 27.346 distance: 127 - 136: 21.371 distance: 128 - 160: 12.036 distance: 129 - 130: 25.479 distance: 130 - 131: 4.420 distance: 131 - 132: 5.849 distance: 132 - 133: 4.268 distance: 133 - 134: 3.621 distance: 133 - 135: 3.713