Starting phenix.real_space_refine on Sun Aug 24 19:04:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfe_19118/08_2025/8rfe_19118.map" } resolution = 3.8 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= 0.004 sd= 0.054 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 6 5.49 5 S 68 5.16 5 C 13717 2.51 5 N 3864 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21776 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 21580 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 22028 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'UPG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 9.53, per 1000 atoms: 0.44 Number of scatterers: 21776 At special positions: 0 Unit cell: (103.777, 120.433, 210.117, 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 68 16.00 P 6 15.00 O 4121 8.00 N 3864 7.00 C 13717 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 Links applied BETA1-2 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC B 5 " - " BGC B 6 " " BGC B 6 " - " BGC B 7 " " BGC B 7 " - " BGC B 8 " " BGC B 8 " - " BGC B 9 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 22 sheets defined 46.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.351A pdb=" N ASP A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 79 removed outlier: 5.481A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.571A pdb=" N ILE A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.872A pdb=" N GLY A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.886A pdb=" N LEU A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 172 through 212 removed outlier: 3.877A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.501A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.661A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.894A pdb=" N GLU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 267 through 274 removed outlier: 3.692A pdb=" N GLU A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.706A pdb=" N LYS A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.488A pdb=" N GLU A 321 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.501A pdb=" N LEU A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 394 through 406 Processing helix chain 'A' and resid 408 through 430 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 449 through 467 Processing helix chain 'A' and resid 500 through 515 removed outlier: 3.808A pdb=" N ASN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 557 removed outlier: 3.796A pdb=" N ALA A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.598A pdb=" N ARG A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 737 through 745 Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.667A pdb=" N GLY A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 793 through 824 removed outlier: 3.520A pdb=" N ARG A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Proline residue: A 810 - end of helix removed outlier: 4.261A pdb=" N MET A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 849 removed outlier: 3.517A pdb=" N TRP A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 836 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 4.630A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 848 " --> pdb=" O PRO A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 867 through 885 removed outlier: 4.200A pdb=" N GLU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.642A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 Proline residue: A 962 - end of helix removed outlier: 3.595A pdb=" N LEU A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 991 through 1005 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'A' and resid 1037 through 1055 Processing helix chain 'A' and resid 1058 through 1075 Processing helix chain 'A' and resid 1102 through 1124 Processing helix chain 'A' and resid 1135 through 1149 removed outlier: 3.637A pdb=" N LYS A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.547A pdb=" N ARG A1163 " --> pdb=" O ARG A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1211 removed outlier: 3.525A pdb=" N VAL A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.603A pdb=" N VAL A1219 " --> pdb=" O GLN A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1264 Processing helix chain 'A' and resid 1267 through 1271 Processing helix chain 'A' and resid 1300 through 1311 removed outlier: 3.678A pdb=" N THR A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.780A pdb=" N TYR A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1345 Processing helix chain 'A' and resid 1346 through 1352 removed outlier: 3.747A pdb=" N VAL A1351 " --> pdb=" O MET A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1379 Processing helix chain 'A' and resid 1405 through 1409 removed outlier: 3.896A pdb=" N GLY A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 4.191A pdb=" N SER A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1426 " --> pdb=" O PRO A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1445 Processing helix chain 'A' and resid 1461 through 1465 Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1503 Processing helix chain 'A' and resid 1505 through 1513 removed outlier: 3.978A pdb=" N LEU A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1542 removed outlier: 3.995A pdb=" N LEU A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1696 removed outlier: 3.522A pdb=" N HIS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1703 removed outlier: 3.830A pdb=" N SER A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1756 removed outlier: 3.536A pdb=" N GLY A1756 " --> pdb=" O ALA A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1768 removed outlier: 3.766A pdb=" N PHE A1767 " --> pdb=" O ALA A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1823 removed outlier: 3.676A pdb=" N ALA A1817 " --> pdb=" O GLU A1813 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A1823 " --> pdb=" O ASP A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1845 removed outlier: 3.993A pdb=" N VAL A1845 " --> pdb=" O GLN A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1864 removed outlier: 3.643A pdb=" N TYR A1861 " --> pdb=" O HIS A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1878 removed outlier: 3.887A pdb=" N THR A1878 " --> pdb=" O THR A1875 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1887 Processing helix chain 'A' and resid 1909 through 1925 removed outlier: 3.647A pdb=" N GLU A1913 " --> pdb=" O ASP A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1953 removed outlier: 3.670A pdb=" N ILE A1951 " --> pdb=" O ALA A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1988 Processing helix chain 'A' and resid 2001 through 2010 Processing helix chain 'A' and resid 2212 through 2216 removed outlier: 3.797A pdb=" N ILE A2216 " --> pdb=" O ALA A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2316 through 2330 removed outlier: 3.783A pdb=" N GLN A2329 " --> pdb=" O LYS A2325 " (cutoff:3.500A) Processing helix chain 'A' and resid 2332 through 2348 removed outlier: 3.616A pdb=" N LEU A2336 " --> pdb=" O PHE A2332 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2363 removed outlier: 3.511A pdb=" N VAL A2363 " --> pdb=" O PHE A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2375 Processing helix chain 'A' and resid 2391 through 2398 removed outlier: 4.574A pdb=" N THR A2398 " --> pdb=" O GLN A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 2443 through 2460 removed outlier: 4.473A pdb=" N VAL A2447 " --> pdb=" O SER A2443 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) Processing helix chain 'A' and resid 2463 through 2467 Processing helix chain 'A' and resid 2497 through 2512 Processing helix chain 'A' and resid 2542 through 2563 removed outlier: 3.968A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2585 removed outlier: 4.123A pdb=" N LYS A2570 " --> pdb=" O ASP A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2625 removed outlier: 4.177A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A2625 " --> pdb=" O SER A2621 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2640 Processing helix chain 'A' and resid 2641 through 2644 removed outlier: 3.676A pdb=" N VAL A2644 " --> pdb=" O GLU A2641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2641 through 2644' Processing helix chain 'A' and resid 2667 through 2671 Processing helix chain 'A' and resid 2683 through 2697 removed outlier: 3.644A pdb=" N TRP A2688 " --> pdb=" O HIS A2684 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A2697 " --> pdb=" O LEU A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2710 Processing helix chain 'A' and resid 2738 through 2742 removed outlier: 3.983A pdb=" N TYR A2741 " --> pdb=" O GLU A2738 " (cutoff:3.500A) Processing helix chain 'A' and resid 2753 through 2764 Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 removed outlier: 9.314A pdb=" N TYR A 566 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 522 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU A 568 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 524 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR A 487 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 523 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 489 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 525 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 491 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 628 through 629 removed outlier: 3.847A pdb=" N VAL A 757 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA4, first strand: chain 'A' and resid 1023 through 1025 Processing sheet with id=AA5, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA6, first strand: chain 'A' and resid 1099 through 1101 Processing sheet with id=AA7, first strand: chain 'A' and resid 1326 through 1329 removed outlier: 3.520A pdb=" N GLN A1332 " --> pdb=" O ILE A1329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1419 through 1420 Processing sheet with id=AA9, first strand: chain 'A' and resid 1449 through 1450 removed outlier: 3.535A pdb=" N GLY A1453 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1548 through 1550 removed outlier: 3.516A pdb=" N ARG A1548 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1560 through 1564 removed outlier: 6.581A pdb=" N SER A1580 " --> pdb=" O ILE A1587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1585 " --> pdb=" O TRP A1582 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A1585 " --> pdb=" O ALA A1688 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A1688 " --> pdb=" O GLN A1585 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.505A pdb=" N LEU A1787 " --> pdb=" O SER A1681 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1968 through 1972 removed outlier: 6.023A pdb=" N PHE A1898 " --> pdb=" O VAL A1931 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A1933 " --> pdb=" O PHE A1898 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A1900 " --> pdb=" O VAL A1933 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1992 " --> pdb=" O SER A1899 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2051 through 2053 Processing sheet with id=AB6, first strand: chain 'A' and resid 2076 through 2080 removed outlier: 3.974A pdb=" N PHE A2083 " --> pdb=" O ASN A2080 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2119 through 2120 removed outlier: 3.504A pdb=" N ALA A2199 " --> pdb=" O LEU A2293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2351 through 2352 Processing sheet with id=AB9, first strand: chain 'A' and resid 2389 through 2390 removed outlier: 3.567A pdb=" N TRP A2430 " --> pdb=" O PHE A2389 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2473 through 2474 Processing sheet with id=AC2, first strand: chain 'A' and resid 2540 through 2541 Processing sheet with id=AC3, first strand: chain 'A' and resid 2681 through 2682 removed outlier: 3.649A pdb=" N VAL A2735 " --> pdb=" O GLN A2681 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A2732 " --> pdb=" O SER A2748 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER A2748 " --> pdb=" O THR A2732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2768 through 2770 997 hydrogen bonds defined for protein. 2848 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: 6.65 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7327 1.34 - 1.46: 5131 1.46 - 1.58: 9686 1.58 - 1.70: 12 1.70 - 1.82: 121 Bond restraints: 22277 Sorted by residual: bond pdb=" C1 BGC B 2 " pdb=" O5 BGC B 2 " ideal model delta sigma weight residual 1.408 1.476 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 BGC B 9 " pdb=" O5 BGC B 9 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" N GLU A1228 " pdb=" CA GLU A1228 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.11e+00 bond pdb=" O3B UPG A2903 " pdb=" PB UPG A2903 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" O3B UPG A2902 " pdb=" PB UPG A2902 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 22272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 29675 1.86 - 3.72: 494 3.72 - 5.58: 85 5.58 - 7.44: 28 7.44 - 9.31: 7 Bond angle restraints: 30289 Sorted by residual: angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.79 109.83 -7.04 6.60e-01 2.30e+00 1.14e+02 angle pdb=" N PRO A2033 " pdb=" CA PRO A2033 " pdb=" CB PRO A2033 " ideal model delta sigma weight residual 103.25 110.86 -7.61 1.05e+00 9.07e-01 5.26e+01 angle pdb=" N PRO A1524 " pdb=" CA PRO A1524 " pdb=" CB PRO A1524 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.20e+01 angle pdb=" N PRO A1888 " pdb=" CA PRO A1888 " pdb=" CB PRO A1888 " ideal model delta sigma weight residual 103.25 110.18 -6.93 1.05e+00 9.07e-01 4.36e+01 angle pdb=" N PRO A2028 " pdb=" CA PRO A2028 " pdb=" CB PRO A2028 " ideal model delta sigma weight residual 103.25 110.08 -6.83 1.05e+00 9.07e-01 4.23e+01 ... (remaining 30284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 12584 25.70 - 51.40: 663 51.40 - 77.11: 58 77.11 - 102.81: 34 102.81 - 128.51: 34 Dihedral angle restraints: 13373 sinusoidal: 5384 harmonic: 7989 Sorted by residual: dihedral pdb=" CA VAL A 72 " pdb=" C VAL A 72 " pdb=" N TYR A 73 " pdb=" CA TYR A 73 " ideal model delta harmonic sigma weight residual 180.00 140.21 39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA ALA A1519 " pdb=" C ALA A1519 " pdb=" N PRO A1520 " pdb=" CA PRO A1520 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C2 BGC B 1 " pdb=" C1 BGC B 1 " pdb=" O5 BGC B 1 " pdb=" C5 BGC B 1 " ideal model delta sinusoidal sigma weight residual -65.02 63.49 -128.51 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 13370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2776 0.053 - 0.105: 506 0.105 - 0.158: 68 0.158 - 0.210: 6 0.210 - 0.263: 6 Chirality restraints: 3362 Sorted by residual: chirality pdb=" CA PRO A1888 " pdb=" N PRO A1888 " pdb=" C PRO A1888 " pdb=" CB PRO A1888 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO A2037 " pdb=" N PRO A2037 " pdb=" C PRO A2037 " pdb=" CB PRO A2037 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A2030 " pdb=" N PRO A2030 " pdb=" C PRO A2030 " pdb=" CB PRO A2030 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3359 not shown) Planarity restraints: 3929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 821 " -0.025 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP A 821 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 821 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 821 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 821 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 821 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 821 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 821 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 821 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 821 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1865 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO A1865 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO A1865 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A1866 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1519 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C ALA A1519 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA A1519 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A1520 " 0.021 2.00e-02 2.50e+03 ... (remaining 3926 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 628 2.70 - 3.25: 22321 3.25 - 3.80: 35439 3.80 - 4.35: 44179 4.35 - 4.90: 72335 Nonbonded interactions: 174902 Sorted by model distance: nonbonded pdb=" O VAL A2077 " pdb=" OH TYR A2369 " model vdw 2.148 3.040 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.158 3.040 nonbonded pdb=" O PRO A 844 " pdb=" OG SER A 847 " model vdw 2.180 3.040 nonbonded pdb=" O ALA A 552 " pdb=" OG SER A 555 " model vdw 2.192 3.040 nonbonded pdb=" O HIS A2580 " pdb=" OG1 THR A2584 " model vdw 2.196 3.040 ... (remaining 174897 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=0.40 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 30.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.003 0.068 22285 Z= 0.144 Angle : 0.608 9.305 30313 Z= 0.327 Chirality : 0.042 0.263 3362 Planarity : 0.003 0.053 3929 Dihedral : 16.601 128.510 8231 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.61 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.82 (0.17), residues: 2759 helix: 1.23 (0.16), residues: 1154 sheet: 0.21 (0.30), residues: 329 loop : -2.58 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1163 TYR 0.015 0.001 TYR A 73 PHE 0.012 0.001 PHE A2547 TRP 0.069 0.001 TRP A 821 HIS 0.004 0.001 HIS A1209 Details of bonding type rmsd covalent geometry : bond 0.00283 (22277) covalent geometry : angle 0.60718 (30289) hydrogen bonds : bond 0.14534 ( 997) hydrogen bonds : angle 5.78995 ( 2848) link_BETA1-2 : bond 0.00528 ( 8) link_BETA1-2 : angle 1.12553 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.892 Fit side-chains REVERT: A 296 ASP cc_start: 0.9266 (m-30) cc_final: 0.9013 (m-30) REVERT: A 423 MET cc_start: 0.9236 (ptp) cc_final: 0.9003 (ppp) REVERT: A 621 MET cc_start: 0.8428 (tpt) cc_final: 0.8214 (tpt) REVERT: A 824 MET cc_start: 0.8763 (pmm) cc_final: 0.8308 (pmm) REVERT: A 1244 MET cc_start: 0.8449 (mmp) cc_final: 0.8118 (mmm) REVERT: A 2135 CYS cc_start: 0.8873 (m) cc_final: 0.8611 (m) REVERT: A 2636 MET cc_start: 0.8856 (mmp) cc_final: 0.7899 (ptm) REVERT: A 2640 MET cc_start: 0.9071 (mmp) cc_final: 0.8784 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1463 time to fit residues: 29.0315 Evaluate side-chains 90 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 55.007 > 50: distance: 27 - 30: 6.750 distance: 30 - 31: 4.068 distance: 31 - 32: 6.344 distance: 31 - 34: 4.499 distance: 32 - 33: 6.436 distance: 35 - 36: 6.647 distance: 36 - 37: 11.570 distance: 36 - 39: 5.856 distance: 37 - 38: 10.745 distance: 37 - 40: 16.886 distance: 40 - 41: 16.952 distance: 41 - 42: 25.622 distance: 41 - 44: 12.028 distance: 42 - 43: 33.583 distance: 42 - 45: 34.925 distance: 45 - 46: 10.221 distance: 46 - 47: 32.711 distance: 46 - 49: 19.162 distance: 47 - 48: 39.479 distance: 47 - 50: 33.871 distance: 50 - 51: 13.350 distance: 51 - 52: 8.458 distance: 51 - 54: 11.545 distance: 52 - 53: 23.290 distance: 52 - 55: 12.039 distance: 55 - 56: 8.917 distance: 56 - 57: 12.229 distance: 56 - 59: 13.319 distance: 57 - 58: 7.370 distance: 57 - 60: 22.956 distance: 60 - 61: 24.204 distance: 61 - 62: 24.282 distance: 61 - 64: 16.662 distance: 62 - 63: 16.269 distance: 62 - 65: 8.652 distance: 65 - 66: 19.326 distance: 66 - 67: 29.246 distance: 66 - 69: 42.925 distance: 67 - 68: 22.002 distance: 67 - 70: 16.626 distance: 70 - 71: 33.325 distance: 71 - 72: 11.319 distance: 71 - 74: 24.720 distance: 72 - 73: 22.010 distance: 72 - 75: 6.545 distance: 75 - 76: 13.966 distance: 76 - 77: 19.383 distance: 76 - 79: 7.991 distance: 77 - 78: 11.250 distance: 77 - 80: 9.246