Starting phenix.real_space_refine on Thu Feb 5 02:31:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1k_63574/02_2026/9m1k_63574.cif" } resolution = 2.45 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 89 5.16 5 C 9036 2.51 5 N 2483 2.21 5 O 2665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14281 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 8647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8647 Classifications: {'peptide': 1103} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1056} Chain breaks: 2 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1466 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "b" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3380 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.24 Number of scatterers: 14281 At special positions: 0 Unit cell: (91.2975, 115.579, 143.745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 89 16.00 P 6 15.00 Mg 2 11.99 O 2665 8.00 N 2483 7.00 C 9036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 565.2 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 6 sheets defined 64.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.902A pdb=" N LYS D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 77 through 87 removed outlier: 4.092A pdb=" N MET D 81 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.774A pdb=" N GLN D 139 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 removed outlier: 3.700A pdb=" N LEU D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 202 through 216 removed outlier: 4.049A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.998A pdb=" N GLN D 222 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 237 Processing helix chain 'D' and resid 243 through 263 Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.797A pdb=" N ALA D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 removed outlier: 3.591A pdb=" N ARG D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.941A pdb=" N ARG D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.637A pdb=" N CYS D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.923A pdb=" N ARG D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 436 through 446 removed outlier: 3.507A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 478 removed outlier: 3.596A pdb=" N ALA D 475 " --> pdb=" O CYS D 471 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 476 " --> pdb=" O TRP D 472 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 478 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'D' and resid 487 through 498 removed outlier: 3.976A pdb=" N ALA D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 555 Processing helix chain 'D' and resid 556 through 559 Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.774A pdb=" N ILE D 564 " --> pdb=" O THR D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 574 removed outlier: 3.618A pdb=" N HIS D 574 " --> pdb=" O LYS D 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 571 through 574' Processing helix chain 'D' and resid 576 through 592 removed outlier: 3.992A pdb=" N GLN D 592 " --> pdb=" O HIS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 601 removed outlier: 3.511A pdb=" N GLN D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 614 through 639 removed outlier: 3.538A pdb=" N ARG D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.538A pdb=" N HIS D 646 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 656 Processing helix chain 'D' and resid 657 through 665 Processing helix chain 'D' and resid 669 through 690 removed outlier: 3.537A pdb=" N GLN D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 681 " --> pdb=" O ARG D 677 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 682 " --> pdb=" O GLN D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.938A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 740 removed outlier: 3.937A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.708A pdb=" N GLN D 759 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 766 No H-bonds generated for 'chain 'D' and resid 764 through 766' Processing helix chain 'D' and resid 768 through 781 Processing helix chain 'D' and resid 790 through 802 removed outlier: 3.540A pdb=" N VAL D 794 " --> pdb=" O ARG D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.701A pdb=" N ARG D 815 " --> pdb=" O PHE D 811 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 857 removed outlier: 3.716A pdb=" N ASP D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 887 removed outlier: 4.040A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 874 " --> pdb=" O TRP D 870 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 885 " --> pdb=" O ASP D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 889 No H-bonds generated for 'chain 'D' and resid 888 through 889' Processing helix chain 'D' and resid 890 through 894 Processing helix chain 'D' and resid 895 through 911 removed outlier: 3.538A pdb=" N CYS D 899 " --> pdb=" O GLU D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 930 Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 961 through 964 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 976 through 978 No H-bonds generated for 'chain 'D' and resid 976 through 978' Processing helix chain 'D' and resid 979 through 991 removed outlier: 4.181A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1011 removed outlier: 4.019A pdb=" N GLY D1011 " --> pdb=" O GLU D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1032 removed outlier: 3.726A pdb=" N LEU D1019 " --> pdb=" O ASP D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1054 removed outlier: 3.778A pdb=" N VAL D1041 " --> pdb=" O GLU D1037 " (cutoff:3.500A) Proline residue: D1042 - end of helix Processing helix chain 'D' and resid 1057 through 1061 Processing helix chain 'D' and resid 1065 through 1080 removed outlier: 3.628A pdb=" N LEU D1071 " --> pdb=" O PHE D1067 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D1072 " --> pdb=" O ALA D1068 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D1077 " --> pdb=" O ALA D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.619A pdb=" N SER D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1102 Proline residue: D1102 - end of helix No H-bonds generated for 'chain 'D' and resid 1099 through 1102' Processing helix chain 'D' and resid 1103 through 1117 removed outlier: 3.562A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.922A pdb=" N ASP D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 3.502A pdb=" N VAL D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 removed outlier: 4.590A pdb=" N LYS G 8 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN G 12 " --> pdb=" O LYS G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.514A pdb=" N ASN G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 75 removed outlier: 4.083A pdb=" N SER G 75 " --> pdb=" O LYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.814A pdb=" N PHE G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 112 removed outlier: 3.600A pdb=" N CYS G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 111 " --> pdb=" O GLN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 removed outlier: 3.700A pdb=" N GLU G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 180 removed outlier: 3.804A pdb=" N GLY G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP G 171 " --> pdb=" O PRO G 167 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 26 Processing helix chain 'b' and resid 46 through 49 Processing helix chain 'b' and resid 69 through 78 removed outlier: 4.392A pdb=" N MET b 73 " --> pdb=" O GLU b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 Processing helix chain 'b' and resid 108 through 127 removed outlier: 3.876A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP b 118 " --> pdb=" O ASP b 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 159 Processing helix chain 'b' and resid 180 through 185 Processing helix chain 'b' and resid 186 through 195 Processing helix chain 'b' and resid 204 through 214 removed outlier: 3.548A pdb=" N TYR b 208 " --> pdb=" O ASN b 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.539A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 242 removed outlier: 3.540A pdb=" N ARG b 241 " --> pdb=" O THR b 237 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 removed outlier: 3.804A pdb=" N PHE b 294 " --> pdb=" O THR b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 322 through 334 Processing helix chain 'b' and resid 371 through 373 No H-bonds generated for 'chain 'b' and resid 371 through 373' Processing helix chain 'b' and resid 374 through 390 removed outlier: 3.515A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA b 387 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N MET b 388 " --> pdb=" O GLN b 384 " (cutoff:3.500A) Processing helix chain 'b' and resid 394 through 400 removed outlier: 4.225A pdb=" N TYR b 398 " --> pdb=" O PHE b 394 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 427 removed outlier: 4.055A pdb=" N ASP b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 461 through 465 removed outlier: 3.927A pdb=" N LEU E 461 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU E 523 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS E 449 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL E 525 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS E 451 " --> pdb=" O VAL E 525 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 503 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.569A pdb=" N GLU D 452 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 50 through 57 removed outlier: 7.133A pdb=" N LEU G 17 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TRP G 65 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 86 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 90 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 91 removed outlier: 8.246A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE b 64 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS b 6 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL b 66 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 8 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU b 3 " --> pdb=" O LEU b 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY b 132 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL b 5 " --> pdb=" O GLY b 132 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ILE b 163 " --> pdb=" O CYS b 129 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN b 131 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU b 198 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA b 352 " --> pdb=" O VAL b 313 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA b 315 " --> pdb=" O ALA b 352 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS b 354 " --> pdb=" O ALA b 315 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE b 317 " --> pdb=" O CYS b 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'b' and resid 169 through 170 741 hydrogen bonds defined for protein. 2157 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: 2.56 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2485 1.32 - 1.44: 3634 1.44 - 1.57: 8295 1.57 - 1.69: 10 1.69 - 1.81: 137 Bond restraints: 14561 Sorted by residual: bond pdb=" C GLN D 302 " pdb=" N ARG D 303 " ideal model delta sigma weight residual 1.335 1.400 -0.065 1.36e-02 5.41e+03 2.29e+01 bond pdb=" C ASP D 501 " pdb=" N ARG D 502 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.42e-02 4.96e+03 2.18e+01 bond pdb=" N ILE b 356 " pdb=" CA ILE b 356 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 1.97e+01 bond pdb=" N VAL b 60 " pdb=" CA VAL b 60 " ideal model delta sigma weight residual 1.457 1.495 -0.037 9.00e-03 1.23e+04 1.72e+01 bond pdb=" O1G GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 14556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 19620 4.19 - 8.37: 108 8.37 - 12.56: 7 12.56 - 16.74: 3 16.74 - 20.93: 2 Bond angle restraints: 19740 Sorted by residual: angle pdb=" CA SER D 933 " pdb=" C SER D 933 " pdb=" N PRO D 934 " ideal model delta sigma weight residual 117.44 123.98 -6.54 9.20e-01 1.18e+00 5.06e+01 angle pdb=" PA GTP G1500 " pdb=" O3A GTP G1500 " pdb=" PB GTP G1500 " ideal model delta sigma weight residual 120.50 141.43 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 140.70 -20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" PB GTP G1500 " pdb=" O3B GTP G1500 " pdb=" PG GTP G1500 " ideal model delta sigma weight residual 120.50 136.62 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sigma weight residual 120.50 136.49 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 19735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 8545 34.18 - 68.36: 221 68.36 - 102.55: 20 102.55 - 136.73: 4 136.73 - 170.91: 5 Dihedral angle restraints: 8795 sinusoidal: 3564 harmonic: 5231 Sorted by residual: dihedral pdb=" C8 GTP G1500 " pdb=" C1' GTP G1500 " pdb=" N9 GTP G1500 " pdb=" O4' GTP G1500 " ideal model delta sinusoidal sigma weight residual 104.59 -66.32 170.91 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O3B GTP G1500 " pdb=" O3A GTP G1500 " pdb=" PB GTP G1500 " pdb=" PA GTP G1500 " ideal model delta sinusoidal sigma weight residual 291.08 129.67 161.41 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C4' GTP b1500 " pdb=" C5' GTP b1500 " pdb=" O5' GTP b1500 " pdb=" PA GTP b1500 " ideal model delta sinusoidal sigma weight residual 260.87 103.67 157.20 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 8792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1671 0.044 - 0.087: 305 0.087 - 0.131: 188 0.131 - 0.175: 67 0.175 - 0.219: 16 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA VAL b 91 " pdb=" N VAL b 91 " pdb=" C VAL b 91 " pdb=" CB VAL b 91 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE D1085 " pdb=" N ILE D1085 " pdb=" C ILE D1085 " pdb=" CB ILE D1085 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' GTP G1500 " pdb=" C2' GTP G1500 " pdb=" C4' GTP G1500 " pdb=" O3' GTP G1500 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2244 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D1036 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ASN D1036 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN D1036 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D1037 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS b 190 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C HIS b 190 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS b 190 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN b 191 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 25 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C SER b 25 " -0.039 2.00e-02 2.50e+03 pdb=" O SER b 25 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP b 26 " 0.013 2.00e-02 2.50e+03 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1403 2.75 - 3.28: 14552 3.28 - 3.82: 23440 3.82 - 4.36: 28554 4.36 - 4.90: 48153 Nonbonded interactions: 116102 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb="MG MG G1501 " model vdw 2.207 2.170 nonbonded pdb=" OD1 ASP D 134 " pdb=" NH2 ARG D 188 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLN b 15 " pdb=" O6 GTP b1500 " model vdw 2.394 3.040 nonbonded pdb=" O1B GTP G1500 " pdb="MG MG G1501 " model vdw 2.455 2.170 nonbonded pdb=" OD1 ASP b 31 " pdb=" O THR b 35 " model vdw 2.497 3.040 ... (remaining 116097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.920 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: 0.010 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14561 Z= 0.448 Angle : 0.908 20.929 19740 Z= 0.606 Chirality : 0.052 0.219 2247 Planarity : 0.003 0.029 2532 Dihedral : 15.893 170.910 5411 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.06 % Allowed : 8.82 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -1.87 (0.19), residues: 1795 helix: -0.38 (0.16), residues: 1047 sheet: -2.12 (0.40), residues: 130 loop : -2.42 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 641 TYR 0.015 0.001 TYR D 196 PHE 0.012 0.001 PHE D 486 TRP 0.007 0.000 TRP b 101 HIS 0.008 0.000 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00611 (14561) covalent geometry : angle 0.90818 (19740) hydrogen bonds : bond 0.18671 ( 741) hydrogen bonds : angle 7.12648 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 510 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8005 (mmmm) REVERT: D 165 PHE cc_start: 0.7219 (m-80) cc_final: 0.6990 (m-80) REVERT: D 565 ASP cc_start: 0.6939 (m-30) cc_final: 0.6665 (m-30) REVERT: D 736 LEU cc_start: 0.7216 (tp) cc_final: 0.6987 (tt) REVERT: D 892 GLU cc_start: 0.7356 (pm20) cc_final: 0.7095 (mp0) REVERT: D 1032 ASP cc_start: 0.6626 (p0) cc_final: 0.5926 (p0) REVERT: G 14 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7060 (mt-10) REVERT: G 56 GLU cc_start: 0.7427 (tp30) cc_final: 0.7201 (tp30) REVERT: b 200 TYR cc_start: 0.8466 (m-80) cc_final: 0.8230 (m-80) REVERT: b 304 ASP cc_start: 0.8083 (t0) cc_final: 0.7813 (t70) outliers start: 1 outliers final: 1 residues processed: 479 average time/residue: 0.6588 time to fit residues: 342.7066 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8885 > 50: distance: 102 - 223: 34.769 distance: 105 - 220: 16.208 distance: 117 - 201: 31.762 distance: 120 - 198: 33.921 distance: 131 - 185: 35.459 distance: 134 - 182: 27.462 distance: 143 - 165: 36.091 distance: 146 - 162: 25.807 distance: 160 - 162: 24.178 distance: 162 - 163: 41.075 distance: 164 - 173: 25.626 distance: 167 - 168: 40.277 distance: 168 - 170: 5.336 distance: 169 - 171: 4.169 distance: 170 - 172: 39.474 distance: 173 - 174: 35.432 distance: 174 - 175: 44.205 distance: 175 - 176: 46.076 distance: 175 - 182: 49.685 distance: 177 - 178: 41.492 distance: 178 - 179: 39.655 distance: 180 - 181: 27.213 distance: 182 - 183: 18.229 distance: 183 - 184: 31.916 distance: 183 - 186: 24.696 distance: 184 - 185: 14.768 distance: 184 - 190: 30.761 distance: 187 - 188: 33.921 distance: 187 - 189: 40.839 distance: 190 - 191: 56.126 distance: 191 - 192: 22.351 distance: 191 - 194: 17.943 distance: 192 - 193: 25.728 distance: 192 - 198: 24.376 distance: 195 - 196: 39.527 distance: 195 - 197: 25.857 distance: 198 - 199: 40.095 distance: 199 - 200: 18.220 distance: 200 - 201: 16.753 distance: 202 - 204: 31.049 distance: 203 - 205: 27.235 distance: 206 - 207: 33.771 distance: 207 - 208: 15.244 distance: 207 - 210: 25.821 distance: 208 - 209: 16.193 distance: 208 - 220: 34.278 distance: 210 - 211: 31.595 distance: 211 - 213: 40.856 distance: 212 - 214: 40.178 distance: 213 - 215: 25.941 distance: 213 - 216: 4.968 distance: 214 - 215: 24.259 distance: 215 - 217: 29.525 distance: 216 - 218: 16.311 distance: 217 - 219: 11.712 distance: 218 - 219: 14.995 distance: 220 - 221: 22.716 distance: 221 - 222: 11.295 distance: 221 - 224: 27.985 distance: 222 - 223: 40.603 distance: 222 - 228: 40.160 distance: 224 - 225: 40.309 distance: 225 - 226: 56.595 distance: 225 - 227: 29.890 distance: 228 - 229: 41.734 distance: 229 - 230: 10.915 distance: 229 - 232: 49.494 distance: 232 - 233: 58.057 distance: 232 - 234: 22.899 distance: 235 - 236: 37.792 distance: 236 - 237: 25.233 distance: 237 - 238: 34.633 distance: 237 - 239: 12.728 distance: 239 - 240: 40.141 distance: 240 - 241: 56.898 distance: 241 - 242: 41.270 distance: 241 - 243: 34.184