Starting phenix.real_space_refine on Sun May 3 16:32:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9c_40239/05_2026/8s9c_40239.cif" } resolution = 3.2 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= -0.002 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 97 5.16 5 C 8944 2.51 5 N 2046 2.21 5 O 2431 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13534 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10262 Classifications: {'peptide': 1273} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 739 Unusual residues: {'LPE': 9, 'N6W': 1, 'NAG': 2, 'PCW': 4, 'Y01': 5} Classifications: {'peptide': 3, 'undetermined': 21} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.25, per 1000 atoms: 0.24 Number of scatterers: 13534 At special positions: 0 Unit cell: (129.224, 138.136, 126.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 16 15.00 O 2431 8.00 N 2046 7.00 C 8944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 639.2 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2972 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 9 sheets defined 65.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.758A pdb=" N PHE A 12 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.005A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.279A pdb=" N ASP A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.522A pdb=" N TYR A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 125 through 143 removed outlier: 3.976A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.194A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.564A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.937A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.619A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.007A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.969A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 418 Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.953A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.925A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 797 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 838 through 847 removed outlier: 4.065A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 4.290A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.596A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 929 through 940 removed outlier: 3.794A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 4.044A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 removed outlier: 3.586A pdb=" N GLU A1212 " --> pdb=" O LEU A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1212' Processing helix chain 'A' and resid 1214 through 1218 removed outlier: 4.266A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 3.533A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1300 removed outlier: 3.589A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.583A pdb=" N ALA A1313 " --> pdb=" O VAL A1309 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.800A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1375 Processing helix chain 'A' and resid 1391 through 1404 removed outlier: 3.566A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 4.131A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.891A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1447 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A1449 " --> pdb=" O SER A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 removed outlier: 3.854A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1487 " --> pdb=" O ASN A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1534 Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.791A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1600 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.013A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.510A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.541A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.606A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.119A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1706 through 1708 No H-bonds generated for 'chain 'A' and resid 1706 through 1708' Processing helix chain 'A' and resid 1732 through 1751 Processing helix chain 'A' and resid 1752 through 1768 removed outlier: 3.684A pdb=" N ALA A1757 " --> pdb=" O ASN A1753 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.155A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.155A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.338A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 83 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.726A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2226 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: 2.35 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2041 1.32 - 1.44: 3693 1.44 - 1.57: 7889 1.57 - 1.69: 32 1.69 - 1.82: 157 Bond restraints: 13812 Sorted by residual: bond pdb=" C TYR A1228 " pdb=" O TYR A1228 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.26e-02 6.30e+03 1.56e+01 bond pdb=" N VAL A1752 " pdb=" CA VAL A1752 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.06e-02 8.90e+03 1.48e+01 bond pdb=" CA ALA A1229 " pdb=" CB ALA A1229 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" O33 LPE A2024 " pdb=" P LPE A2024 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C45 P5S A2004 " pdb=" C46 P5S A2004 " ideal model delta sigma weight residual 1.531 1.463 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 13807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17930 2.14 - 4.27: 611 4.27 - 6.41: 82 6.41 - 8.55: 26 8.55 - 10.68: 7 Bond angle restraints: 18656 Sorted by residual: angle pdb=" N ILE A1745 " pdb=" CA ILE A1745 " pdb=" C ILE A1745 " ideal model delta sigma weight residual 111.00 106.65 4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N VAL A 218 " pdb=" CA VAL A 218 " pdb=" C VAL A 218 " ideal model delta sigma weight residual 113.07 107.71 5.36 1.36e+00 5.41e-01 1.55e+01 angle pdb=" N PHE A1447 " pdb=" CA PHE A1447 " pdb=" C PHE A1447 " ideal model delta sigma weight residual 112.23 107.33 4.90 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N ASN A1450 " pdb=" CA ASN A1450 " pdb=" C ASN A1450 " ideal model delta sigma weight residual 111.36 107.20 4.16 1.09e+00 8.42e-01 1.46e+01 angle pdb=" CA TRP A1245 " pdb=" C TRP A1245 " pdb=" O TRP A1245 " ideal model delta sigma weight residual 120.70 116.78 3.92 1.03e+00 9.43e-01 1.45e+01 ... (remaining 18651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 8404 34.81 - 69.63: 311 69.63 - 104.44: 33 104.44 - 139.25: 16 139.25 - 174.06: 4 Dihedral angle restraints: 8768 sinusoidal: 4173 harmonic: 4595 Sorted by residual: dihedral pdb=" CD ARG A 214 " pdb=" NE ARG A 214 " pdb=" CZ ARG A 214 " pdb=" NH1 ARG A 214 " ideal model delta sinusoidal sigma weight residual 0.00 -81.14 81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" C41 P5S A2013 " pdb=" C42 P5S A2013 " pdb=" C43 P5S A2013 " pdb=" C44 P5S A2013 " ideal model delta sinusoidal sigma weight residual 92.81 -93.13 -174.06 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A2012 " pdb=" C31 PCW A2012 " pdb=" C32 PCW A2012 " pdb=" O2 PCW A2012 " ideal model delta sinusoidal sigma weight residual -168.17 3.67 -171.84 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1577 0.050 - 0.100: 417 0.100 - 0.150: 97 0.150 - 0.200: 21 0.200 - 0.250: 6 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.81e+00 chirality pdb=" CA VAL A 833 " pdb=" N VAL A 833 " pdb=" C VAL A 833 " pdb=" CB VAL A 833 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2115 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.316 2.00e-02 2.50e+03 2.72e-01 9.23e+02 pdb=" C7 NAG D 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.012 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2014 " 0.044 2.00e-02 2.50e+03 2.58e-01 6.63e+02 pdb=" C19 PCW A2014 " -0.285 2.00e-02 2.50e+03 pdb=" C20 PCW A2014 " 0.397 2.00e-02 2.50e+03 pdb=" C21 PCW A2014 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " 0.264 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG B 303 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " -0.375 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " 0.004 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3232 2.79 - 3.32: 12841 3.32 - 3.85: 21641 3.85 - 4.37: 25479 4.37 - 4.90: 44631 Nonbonded interactions: 107824 Sorted by model distance: nonbonded pdb=" O2H LPE A2017 " pdb=" O31 LPE A2017 " model vdw 2.267 3.040 nonbonded pdb=" OG SER B 42 " pdb=" NH2 ARG B 125 " model vdw 2.298 3.120 nonbonded pdb=" NE ARG B 46 " pdb=" OE2 GLU B 48 " model vdw 2.323 3.120 nonbonded pdb=" OG1 THR C 68 " pdb=" OE1 GLU C 77 " model vdw 2.329 3.040 nonbonded pdb=" OE1 GLU A1305 " pdb=" NH1 ARG A1308 " model vdw 2.378 3.120 ... (remaining 107819 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.260 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.070 13834 Z= 0.406 Angle : 0.905 10.683 18711 Z= 0.492 Chirality : 0.050 0.250 2118 Planarity : 0.018 0.485 2208 Dihedral : 18.579 174.065 5763 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.71 % Allowed : 15.67 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.70 (0.22), residues: 1549 helix: 1.46 (0.18), residues: 899 sheet: -1.16 (0.44), residues: 135 loop : -0.78 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 115 TYR 0.019 0.002 TYR A1235 PHE 0.033 0.002 PHE A 739 TRP 0.015 0.001 TRP A1382 HIS 0.008 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00774 (13812) covalent geometry : angle 0.89961 (18656) SS BOND : bond 0.00272 ( 11) SS BOND : angle 0.96377 ( 22) hydrogen bonds : bond 0.13331 ( 775) hydrogen bonds : angle 5.76071 ( 2226) link_BETA1-4 : bond 0.00677 ( 3) link_BETA1-4 : angle 3.10494 ( 9) link_NAG-ASN : bond 0.00281 ( 8) link_NAG-ASN : angle 2.36291 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.458 Fit side-chains REVERT: A 59 LEU cc_start: 0.7498 (mp) cc_final: 0.7140 (mt) REVERT: A 70 MET cc_start: 0.5975 (mmt) cc_final: 0.5408 (mtt) REVERT: A 76 GLU cc_start: 0.8183 (tp30) cc_final: 0.7924 (tp30) REVERT: A 185 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7259 (mmt-90) REVERT: A 190 TRP cc_start: 0.7620 (m-10) cc_final: 0.6894 (m100) REVERT: A 790 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 810 ILE cc_start: 0.7792 (mm) cc_final: 0.7518 (mm) REVERT: A 902 ASP cc_start: 0.8782 (t0) cc_final: 0.8377 (t0) REVERT: A 1322 MET cc_start: 0.8209 (mmm) cc_final: 0.7996 (mmt) REVERT: A 1462 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7296 (mm110) REVERT: B 96 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7397 (mmt180) REVERT: B 183 LYS cc_start: 0.6943 (ptpt) cc_final: 0.6353 (tppt) outliers start: 10 outliers final: 2 residues processed: 243 average time/residue: 0.1121 time to fit residues: 40.2036 Evaluate side-chains 191 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 1240 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 360 GLN A 900 ASN C 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130114 restraints weight = 16996.788| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.88 r_work: 0.3084 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13834 Z= 0.132 Angle : 0.560 8.602 18711 Z= 0.286 Chirality : 0.041 0.234 2118 Planarity : 0.004 0.056 2208 Dihedral : 17.441 176.427 2770 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 14.96 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.22), residues: 1549 helix: 1.93 (0.17), residues: 895 sheet: -0.89 (0.44), residues: 135 loop : -0.47 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1610 TYR 0.018 0.001 TYR A1739 PHE 0.033 0.001 PHE A 739 TRP 0.010 0.001 TRP A1382 HIS 0.005 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00290 (13812) covalent geometry : angle 0.54714 (18656) SS BOND : bond 0.00374 ( 11) SS BOND : angle 1.45003 ( 22) hydrogen bonds : bond 0.04703 ( 775) hydrogen bonds : angle 4.31913 ( 2226) link_BETA1-4 : bond 0.00441 ( 3) link_BETA1-4 : angle 3.47081 ( 9) link_NAG-ASN : bond 0.00408 ( 8) link_NAG-ASN : angle 2.34967 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7480 (mp) cc_final: 0.7190 (mt) REVERT: A 116 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6964 (ttt90) REVERT: A 190 TRP cc_start: 0.7712 (m-10) cc_final: 0.7250 (m100) REVERT: A 403 MET cc_start: 0.8404 (tpp) cc_final: 0.7818 (tpp) REVERT: A 790 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 810 ILE cc_start: 0.8255 (mm) cc_final: 0.8041 (mm) REVERT: A 814 LEU cc_start: 0.8688 (mp) cc_final: 0.8483 (mp) REVERT: A 902 ASP cc_start: 0.8729 (t0) cc_final: 0.8524 (t0) REVERT: A 1193 TRP cc_start: 0.7999 (m-10) cc_final: 0.7626 (m-10) REVERT: A 1240 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: A 1241 MET cc_start: 0.8486 (ttt) cc_final: 0.8286 (ttt) REVERT: A 1305 GLU cc_start: 0.8096 (tp30) cc_final: 0.7413 (tt0) REVERT: A 1462 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7811 (mm110) REVERT: A 1543 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7447 (tpp) REVERT: A 1639 MET cc_start: 0.9033 (mmm) cc_final: 0.8644 (mmt) REVERT: A 1762 ASN cc_start: 0.8794 (m-40) cc_final: 0.8588 (m-40) REVERT: B 96 ARG cc_start: 0.8426 (ttm110) cc_final: 0.7860 (mmt180) REVERT: B 183 LYS cc_start: 0.7218 (ptpt) cc_final: 0.6593 (tppt) outliers start: 26 outliers final: 14 residues processed: 218 average time/residue: 0.1128 time to fit residues: 36.7048 Evaluate side-chains 212 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 265 GLN C 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127909 restraints weight = 17149.376| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.98 r_work: 0.2995 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13834 Z= 0.154 Angle : 0.533 8.055 18711 Z= 0.274 Chirality : 0.040 0.235 2118 Planarity : 0.004 0.051 2208 Dihedral : 16.434 177.610 2769 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.92 % Allowed : 15.10 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.40 (0.22), residues: 1549 helix: 1.97 (0.17), residues: 901 sheet: -0.79 (0.43), residues: 135 loop : -0.43 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.015 0.001 TYR A1739 PHE 0.019 0.001 PHE A 739 TRP 0.012 0.001 TRP A1245 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00362 (13812) covalent geometry : angle 0.52198 (18656) SS BOND : bond 0.00444 ( 11) SS BOND : angle 1.33329 ( 22) hydrogen bonds : bond 0.04608 ( 775) hydrogen bonds : angle 4.15349 ( 2226) link_BETA1-4 : bond 0.00657 ( 3) link_BETA1-4 : angle 3.27379 ( 9) link_NAG-ASN : bond 0.00243 ( 8) link_NAG-ASN : angle 2.07029 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7514 (mp) cc_final: 0.7261 (mt) REVERT: A 70 MET cc_start: 0.7130 (mmt) cc_final: 0.6769 (mtt) REVERT: A 76 GLU cc_start: 0.8254 (tp30) cc_final: 0.7829 (mm-30) REVERT: A 125 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: A 185 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7368 (mmt-90) REVERT: A 190 TRP cc_start: 0.7910 (m-10) cc_final: 0.7393 (m100) REVERT: A 403 MET cc_start: 0.8416 (tpp) cc_final: 0.7829 (tpp) REVERT: A 902 ASP cc_start: 0.8783 (t0) cc_final: 0.8558 (t0) REVERT: A 979 ILE cc_start: 0.2714 (OUTLIER) cc_final: 0.2297 (pt) REVERT: A 1193 TRP cc_start: 0.8014 (m-10) cc_final: 0.7767 (m-10) REVERT: A 1241 MET cc_start: 0.8680 (ttt) cc_final: 0.8441 (ttp) REVERT: A 1305 GLU cc_start: 0.8108 (tp30) cc_final: 0.7607 (tt0) REVERT: A 1462 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7946 (mm110) REVERT: B 96 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8040 (mmt180) REVERT: B 183 LYS cc_start: 0.7277 (ptpt) cc_final: 0.6634 (tppt) REVERT: C 134 ASP cc_start: 0.8184 (t0) cc_final: 0.7829 (t0) outliers start: 41 outliers final: 27 residues processed: 216 average time/residue: 0.1123 time to fit residues: 36.5155 Evaluate side-chains 215 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 171 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126703 restraints weight = 16975.953| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.93 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13834 Z= 0.178 Angle : 0.544 8.062 18711 Z= 0.280 Chirality : 0.041 0.244 2118 Planarity : 0.004 0.047 2208 Dihedral : 15.889 175.862 2769 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.42 % Allowed : 15.67 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.45 (0.22), residues: 1549 helix: 1.96 (0.17), residues: 906 sheet: -0.67 (0.43), residues: 134 loop : -0.35 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 137 TYR 0.016 0.002 TYR A1739 PHE 0.018 0.002 PHE A1440 TRP 0.015 0.001 TRP A1245 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00426 (13812) covalent geometry : angle 0.53359 (18656) SS BOND : bond 0.00272 ( 11) SS BOND : angle 1.22462 ( 22) hydrogen bonds : bond 0.04736 ( 775) hydrogen bonds : angle 4.12471 ( 2226) link_BETA1-4 : bond 0.00603 ( 3) link_BETA1-4 : angle 3.30621 ( 9) link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 2.07893 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7530 (mp) cc_final: 0.7163 (mt) REVERT: A 70 MET cc_start: 0.7069 (mmt) cc_final: 0.6417 (mtt) REVERT: A 76 GLU cc_start: 0.8485 (tp30) cc_final: 0.8276 (mm-30) REVERT: A 125 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: A 185 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7244 (mmt-90) REVERT: A 190 TRP cc_start: 0.7924 (m-10) cc_final: 0.7386 (m100) REVERT: A 802 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: A 902 ASP cc_start: 0.8813 (t0) cc_final: 0.8548 (t0) REVERT: A 1193 TRP cc_start: 0.7990 (m-10) cc_final: 0.7599 (m-10) REVERT: A 1241 MET cc_start: 0.8671 (ttt) cc_final: 0.8449 (ttp) REVERT: A 1305 GLU cc_start: 0.8098 (tp30) cc_final: 0.7617 (tt0) REVERT: B 96 ARG cc_start: 0.8498 (ttm110) cc_final: 0.7971 (mmt180) REVERT: B 183 LYS cc_start: 0.7299 (ptpt) cc_final: 0.6622 (tppt) REVERT: C 134 ASP cc_start: 0.8229 (t0) cc_final: 0.7850 (t0) REVERT: C 137 ARG cc_start: 0.7729 (ttt-90) cc_final: 0.6989 (ttp80) outliers start: 48 outliers final: 34 residues processed: 215 average time/residue: 0.1051 time to fit residues: 34.3789 Evaluate side-chains 217 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129508 restraints weight = 17037.576| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.90 r_work: 0.2987 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13834 Z= 0.111 Angle : 0.483 7.523 18711 Z= 0.249 Chirality : 0.039 0.213 2118 Planarity : 0.003 0.043 2208 Dihedral : 15.079 172.137 2769 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.28 % Allowed : 16.17 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.74 (0.22), residues: 1549 helix: 2.19 (0.17), residues: 905 sheet: -0.56 (0.43), residues: 135 loop : -0.21 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.016 0.001 TYR A1739 PHE 0.016 0.001 PHE A1263 TRP 0.008 0.001 TRP A1382 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00248 (13812) covalent geometry : angle 0.47348 (18656) SS BOND : bond 0.00233 ( 11) SS BOND : angle 1.02338 ( 22) hydrogen bonds : bond 0.03949 ( 775) hydrogen bonds : angle 3.93354 ( 2226) link_BETA1-4 : bond 0.00616 ( 3) link_BETA1-4 : angle 2.98825 ( 9) link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 1.89895 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7450 (mp) cc_final: 0.7094 (mt) REVERT: A 70 MET cc_start: 0.7140 (mmt) cc_final: 0.6500 (mtt) REVERT: A 76 GLU cc_start: 0.8262 (tp30) cc_final: 0.8045 (mm-30) REVERT: A 125 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7304 (t-90) REVERT: A 185 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7780 (mmt-90) REVERT: A 190 TRP cc_start: 0.7901 (m-10) cc_final: 0.7331 (m100) REVERT: A 814 LEU cc_start: 0.8815 (mp) cc_final: 0.8565 (mp) REVERT: A 902 ASP cc_start: 0.8773 (t0) cc_final: 0.8446 (t0) REVERT: A 979 ILE cc_start: 0.3066 (OUTLIER) cc_final: 0.2702 (pt) REVERT: A 1193 TRP cc_start: 0.7950 (m-10) cc_final: 0.7535 (m-10) REVERT: A 1483 ASN cc_start: 0.8390 (t0) cc_final: 0.8014 (m-40) REVERT: A 1543 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7622 (ttt) REVERT: B 96 ARG cc_start: 0.8393 (ttm110) cc_final: 0.7975 (mtt180) REVERT: B 183 LYS cc_start: 0.7292 (ptpt) cc_final: 0.6614 (tppt) REVERT: C 134 ASP cc_start: 0.8198 (t0) cc_final: 0.7799 (t0) REVERT: C 137 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7440 (ttp80) outliers start: 46 outliers final: 28 residues processed: 223 average time/residue: 0.0962 time to fit residues: 33.1414 Evaluate side-chains 218 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8018 > 50: distance: 62 - 83: 9.741 distance: 66 - 89: 27.512 distance: 74 - 97: 34.312 distance: 78 - 83: 10.078 distance: 79 - 106: 10.396 distance: 83 - 84: 5.810 distance: 84 - 85: 8.319 distance: 84 - 87: 8.148 distance: 85 - 86: 10.181 distance: 85 - 89: 7.237 distance: 86 - 113: 10.250 distance: 87 - 88: 8.203 distance: 88 - 149: 6.194 distance: 89 - 90: 9.869 distance: 90 - 91: 28.520 distance: 90 - 93: 11.051 distance: 91 - 92: 20.333 distance: 91 - 97: 37.379 distance: 92 - 118: 10.698 distance: 93 - 94: 6.455 distance: 94 - 95: 9.660 distance: 95 - 96: 17.935 distance: 97 - 98: 52.347 distance: 98 - 101: 13.674 distance: 99 - 100: 21.097 distance: 99 - 106: 19.672 distance: 101 - 102: 12.596 distance: 102 - 103: 21.272 distance: 103 - 105: 15.212 distance: 106 - 107: 24.276 distance: 107 - 108: 11.810 distance: 107 - 110: 8.361 distance: 108 - 109: 26.563 distance: 108 - 113: 7.285 distance: 110 - 111: 3.721 distance: 110 - 112: 11.153 distance: 113 - 114: 15.223 distance: 114 - 115: 15.342 distance: 114 - 117: 4.133 distance: 115 - 116: 18.637 distance: 115 - 118: 13.076 distance: 118 - 119: 6.766 distance: 119 - 120: 12.905 distance: 120 - 121: 13.781 distance: 120 - 122: 13.859 distance: 121 - 144: 9.540 distance: 122 - 123: 6.709 distance: 123 - 124: 10.393 distance: 123 - 126: 6.355 distance: 124 - 125: 6.852 distance: 124 - 131: 7.651 distance: 125 - 150: 17.667 distance: 126 - 127: 7.164 distance: 127 - 128: 16.741 distance: 128 - 129: 16.681 distance: 128 - 130: 16.935 distance: 131 - 132: 9.165 distance: 132 - 135: 8.156 distance: 133 - 136: 9.435 distance: 134 - 158: 7.429 distance: 136 - 137: 3.268 distance: 137 - 138: 4.492 distance: 137 - 140: 7.673 distance: 138 - 139: 18.815 distance: 138 - 144: 11.049 distance: 139 - 166: 22.149 distance: 140 - 141: 15.197 distance: 141 - 142: 9.432 distance: 142 - 143: 20.661 distance: 144 - 145: 6.864 distance: 145 - 146: 4.106 distance: 145 - 148: 4.538 distance: 146 - 147: 6.870 distance: 146 - 150: 10.304 distance: 147 - 172: 9.395 distance: 148 - 149: 14.140