Starting phenix.real_space_refine on Fri Jul 3 04:08:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.map" model { file = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6roi_4973/07_2026/6roi_4973.cif" } resolution = 3.7 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= 0.004 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Be 1 3.05 5 C 7599 2.51 5 N 1907 2.21 5 O 2213 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 11775 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8861 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 30, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2754 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 21, 'TRANS': 317} Chain: "B" 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 chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.18 Number of scatterers: 11775 At special positions: 0 Unit cell: (74.313, 99.084, 174.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2213 8.00 N 1907 7.00 C 7599 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 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=1, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 439.0 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 38.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 213 through 223 removed outlier: 4.330A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.791A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.901A pdb=" N VAL A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 4.696A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.228A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.644A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.606A pdb=" N LEU A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 481 " --> pdb=" O SER A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.602A pdb=" N PHE A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.773A pdb=" N TYR A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 530 removed outlier: 6.575A pdb=" N ASP A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 530' Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.574A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.785A pdb=" N LEU A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 3.591A pdb=" N THR A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.923A pdb=" N CYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.825A pdb=" N GLN A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.664A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 779 removed outlier: 3.619A pdb=" N TYR A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 removed outlier: 4.981A pdb=" N ASP A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.836A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.657A pdb=" N ALA A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.619A pdb=" N ASN A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.561A pdb=" N GLY A 903 " --> pdb=" O GLY A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 903' Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.563A pdb=" N GLN A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.798A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 1007 removed outlier: 3.874A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A1004 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.913A pdb=" N ALA A1011 " --> pdb=" O ARG A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.937A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 removed outlier: 3.545A pdb=" N MET A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 removed outlier: 3.794A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.795A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1086 removed outlier: 3.955A pdb=" N LYS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 4.623A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 removed outlier: 3.569A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1110 through 1115' Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 3.649A pdb=" N VAL A1136 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1148 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1165 removed outlier: 3.734A pdb=" N ALA A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1182 removed outlier: 3.663A pdb=" N ILE A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1194 through 1201 removed outlier: 3.532A pdb=" N GLY A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1230 removed outlier: 3.959A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 3.699A pdb=" N ALA A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.649A pdb=" N LYS A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.376A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.702A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.679A pdb=" N ARG C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.632A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 346 removed outlier: 3.670A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.710A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE A 307 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.780A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 406 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.579A pdb=" N ILE A 985 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 898 " --> pdb=" O ILE A 861 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 583 removed outlier: 7.016A pdb=" N LYS A 812 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 569 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU A 810 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU A 571 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA A 808 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N LYS A 573 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N ALA A 806 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N CYS A 575 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N ILE A 804 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 12.060A pdb=" N ILE A 577 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 14.708A pdb=" N ILE A 802 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.620A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 111 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 140 Processing sheet with id=AB2, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.268A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 318 hydrogen bonds defined for protein. 888 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: 1.65 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1908 1.31 - 1.44: 3273 1.44 - 1.57: 6774 1.57 - 1.70: 3 1.70 - 1.82: 79 Bond restraints: 12037 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.515 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C10 2Y5 A1502 " pdb=" O16 2Y5 A1502 " ideal model delta sigma weight residual 1.333 1.404 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C11 2Y5 A1502 " pdb=" O18 2Y5 A1502 " ideal model delta sigma weight residual 1.335 1.403 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 2Y5 A1502 " pdb=" P4 2Y5 A1502 " ideal model delta sigma weight residual 1.703 1.646 0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 12032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 15955 2.95 - 5.91: 302 5.91 - 8.86: 38 8.86 - 11.82: 8 11.82 - 14.77: 3 Bond angle restraints: 16306 Sorted by residual: angle pdb=" N GLY A1283 " pdb=" CA GLY A1283 " pdb=" C GLY A1283 " ideal model delta sigma weight residual 115.80 105.83 9.97 1.74e+00 3.30e-01 3.29e+01 angle pdb=" CA TYR A1192 " pdb=" CB TYR A1192 " pdb=" CG TYR A1192 " ideal model delta sigma weight residual 113.90 123.25 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" O1 2Y5 A1502 " pdb=" P1 2Y5 A1502 " pdb=" O13 2Y5 A1502 " ideal model delta sigma weight residual 97.01 111.78 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CA ASN A1033 " pdb=" CB ASN A1033 " pdb=" CG ASN A1033 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N ILE A 671 " pdb=" CA ILE A 671 " pdb=" C ILE A 671 " ideal model delta sigma weight residual 109.34 118.42 -9.08 2.08e+00 2.31e-01 1.91e+01 ... (remaining 16301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 6615 24.33 - 48.65: 468 48.65 - 72.97: 57 72.97 - 97.30: 20 97.30 - 121.62: 9 Dihedral angle restraints: 7169 sinusoidal: 2928 harmonic: 4241 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A1191 " pdb=" C GLU A1191 " pdb=" N TYR A1192 " pdb=" CA TYR A1192 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A1031 " pdb=" C PHE A1031 " pdb=" N ALA A1032 " pdb=" CA ALA A1032 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 7166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.998: 1856 0.998 - 1.996: 0 1.996 - 2.994: 0 2.994 - 3.992: 0 3.992 - 4.990: 1 Chirality restraints: 1857 Sorted by residual: chirality pdb=" C1 2Y5 A1502 " pdb=" C2 2Y5 A1502 " pdb=" C6 2Y5 A1502 " pdb=" O1 2Y5 A1502 " both_signs ideal model delta sigma weight residual False -2.53 2.46 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 199 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1854 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 342 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" CD GLU A 342 " -0.083 2.00e-02 2.50e+03 pdb=" OE1 GLU A 342 " 0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU A 342 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A1058 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1212 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A1213 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " -0.040 5.00e-02 4.00e+02 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 5788 2.99 - 3.62: 16946 3.62 - 4.26: 26595 4.26 - 4.90: 43776 Nonbonded interactions: 93128 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A1501 " model vdw 1.709 2.120 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1601 " model vdw 1.740 2.170 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1602 " model vdw 1.805 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1501 " model vdw 1.999 2.170 nonbonded pdb=" OD2 BFD A 560 " pdb="MG MG A1501 " model vdw 2.076 2.170 ... (remaining 93123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.222 12047 Z= 0.377 Angle : 1.056 14.769 16331 Z= 0.561 Chirality : 0.131 4.990 1857 Planarity : 0.007 0.095 2039 Dihedral : 17.309 121.624 4429 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.23 % Allowed : 9.47 % Favored : 90.30 % 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: -5.18 (0.16), residues: 1438 helix: -4.68 (0.08), residues: 537 sheet: -2.28 (0.33), residues: 201 loop : -2.65 (0.18), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1219 TYR 0.046 0.002 TYR A1192 PHE 0.042 0.003 PHE A 605 TRP 0.047 0.003 TRP C 111 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.38 (12037) covalent geometry : angle 1.04692 / 0.56 (16306) SS BOND : bond 0.01350 / 0.96 ( 2) SS BOND : angle 1.86357 / 1.11 ( 4) hydrogen bonds : bond 0.29893 / 19.40 ( 318) hydrogen bonds : angle 10.78002 / 7.43 ( 888) Misc. bond : bond 0.00488 / 0.33 ( 1) link_BETA1-3 : bond 0.00182 / 0.12 ( 1) link_BETA1-3 : angle 3.61286 / 2.19 ( 3) link_BETA1-4 : bond 0.00756 / 0.46 ( 3) link_BETA1-4 : angle 1.17816 / 0.81 ( 9) link_NAG-ASN : bond 0.00775 / 0.52 ( 3) link_NAG-ASN : angle 5.38194 / 3.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.5012 (tpt) cc_final: 0.4486 (ptt) REVERT: A 272 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7155 (ttp-110) REVERT: A 321 ILE cc_start: 0.7668 (mm) cc_final: 0.7235 (pt) REVERT: A 349 GLN cc_start: 0.7769 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 366 MET cc_start: 0.7363 (mmp) cc_final: 0.7149 (mmt) REVERT: A 382 TYR cc_start: 0.8671 (t80) cc_final: 0.8170 (t80) REVERT: A 660 GLN cc_start: 0.8512 (tp40) cc_final: 0.8299 (tp40) REVERT: A 721 LYS cc_start: 0.7800 (pttt) cc_final: 0.7386 (pttp) REVERT: A 729 GLU cc_start: 0.8373 (mp0) cc_final: 0.8153 (mp0) REVERT: A 744 ARG cc_start: 0.7889 (tpt-90) cc_final: 0.6888 (tpm170) REVERT: A 748 ASP cc_start: 0.8501 (t0) cc_final: 0.8046 (t0) REVERT: A 792 GLU cc_start: 0.8779 (tp30) cc_final: 0.8571 (tp30) REVERT: A 810 GLU cc_start: 0.8831 (pp20) cc_final: 0.7970 (pp20) REVERT: A 819 GLU cc_start: 0.7991 (mp0) cc_final: 0.7558 (tp30) REVERT: A 844 ASN cc_start: 0.8448 (t0) cc_final: 0.8198 (t0) REVERT: A 900 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7408 (pttp) REVERT: A 928 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7318 (ttm-80) REVERT: A 944 LYS cc_start: 0.7928 (tppp) cc_final: 0.7254 (tptt) REVERT: A 1024 MET cc_start: 0.8066 (mmp) cc_final: 0.7808 (tpt) REVERT: A 1087 GLN cc_start: 0.7727 (mt0) cc_final: 0.7256 (tt0) REVERT: A 1159 LYS cc_start: 0.8678 (pttt) cc_final: 0.8212 (tptt) REVERT: A 1188 ILE cc_start: 0.7654 (tp) cc_final: 0.7318 (tp) REVERT: C 168 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7667 (pttp) REVERT: C 220 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8782 (mttm) outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.1038 time to fit residues: 34.0936 Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 898 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 54.5692 > 50: distance: 31 - 41: 3.110 distance: 64 - 84: 25.474 distance: 72 - 77: 3.727 distance: 77 - 78: 8.644 distance: 78 - 79: 3.091 distance: 78 - 81: 4.063 distance: 79 - 80: 31.813 distance: 79 - 84: 23.420 distance: 81 - 82: 10.417 distance: 81 - 83: 17.341 distance: 84 - 85: 13.184 distance: 85 - 86: 13.577 distance: 85 - 88: 5.843 distance: 86 - 87: 6.964 distance: 88 - 89: 13.739 distance: 89 - 90: 9.678 distance: 89 - 91: 7.332 distance: 92 - 93: 5.773 distance: 92 - 98: 4.751 distance: 93 - 94: 5.076 distance: 93 - 96: 9.568 distance: 94 - 99: 4.105 distance: 95 - 123: 3.122 distance: 96 - 97: 3.010 distance: 97 - 98: 10.590 distance: 99 - 100: 3.556 distance: 100 - 101: 3.012 distance: 100 - 103: 6.451 distance: 101 - 102: 4.616 distance: 101 - 107: 6.929 distance: 102 - 131: 4.240 distance: 103 - 104: 5.873 distance: 103 - 105: 7.510 distance: 104 - 106: 9.387 distance: 108 - 109: 4.983 distance: 108 - 111: 6.244 distance: 109 - 118: 4.555 distance: 111 - 112: 6.572 distance: 112 - 113: 6.940 distance: 112 - 114: 3.391 distance: 113 - 115: 3.975 distance: 114 - 116: 4.229 distance: 118 - 119: 5.467 distance: 119 - 120: 3.599 distance: 119 - 122: 5.629 distance: 120 - 121: 5.155 distance: 120 - 123: 4.033 distance: 123 - 124: 6.702 distance: 124 - 125: 3.157 distance: 124 - 127: 3.573 distance: 125 - 126: 6.116 distance: 125 - 131: 4.267 distance: 126 - 157: 8.058 distance: 127 - 128: 4.375 distance: 128 - 129: 5.182 distance: 132 - 133: 3.622 distance: 132 - 135: 4.857 distance: 133 - 134: 6.921 distance: 133 - 138: 3.800 distance: 134 - 163: 3.845 distance: 135 - 136: 7.082 distance: 135 - 137: 5.982 distance: 138 - 139: 6.256 distance: 139 - 142: 5.223 distance: 140 - 141: 8.770 distance: 140 - 149: 5.802 distance: 141 - 170: 6.477 distance: 142 - 143: 6.397 distance: 143 - 144: 8.574 distance: 144 - 145: 9.498 distance: 145 - 146: 8.676 distance: 146 - 147: 18.966 distance: 146 - 148: 4.744 distance: 149 - 150: 3.788 distance: 150 - 151: 4.239 distance: 150 - 153: 4.735 distance: 151 - 152: 3.731 distance: 153 - 154: 5.271 distance: 154 - 156: 4.119