Starting phenix.real_space_refine on Mon Aug 25 00:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nt6_12584/08_2025/7nt6_12584.map" } resolution = 4.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 90 5.49 5 C 11974 2.51 5 N 5762 2.21 5 O 6302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 24128 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 1320 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 309} Link IDs: {'PTRANS': 15, 'TRANS': 314} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1316 Unresolved non-hydrogen angles: 1903 Unresolved non-hydrogen dihedrals: 837 Unresolved non-hydrogen chiralities: 411 Planarities with less than four sites: {'ARG:plan': 22, 'PHE:plan': 14, 'ASN:plan1': 10, 'GLU:plan': 25, 'TRP:plan': 5, 'ASP:plan': 11, 'TYR:plan': 10, 'GLN:plan1': 10} Unresolved non-hydrogen planarities: 562 Chain: "B" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 1444 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 338} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1433 Unresolved non-hydrogen angles: 2070 Unresolved non-hydrogen dihedrals: 913 Unresolved non-hydrogen chiralities: 445 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 26, 'ARG:plan': 26, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 622 Chain: "C" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 1472 Classifications: {'peptide': 368} Incomplete info: {'backbone_only': 344} Link IDs: {'PTRANS': 15, 'TRANS': 352} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 2113 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 451 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 646 Chain: "D" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 1472 Classifications: {'peptide': 368} Incomplete info: {'backbone_only': 344} Link IDs: {'PTRANS': 15, 'TRANS': 352} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 2113 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 451 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 646 Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 1528 Classifications: {'peptide': 382} Incomplete info: {'backbone_only': 356} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1508 Unresolved non-hydrogen angles: 2178 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 466 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 13, 'ASP:plan': 15, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 670 Chain: "F" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 1552 Classifications: {'peptide': 388} Incomplete info: {'backbone_only': 362} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1525 Unresolved non-hydrogen angles: 2204 Unresolved non-hydrogen dihedrals: 965 Unresolved non-hydrogen chiralities: 473 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 29, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 14, 'ASP:plan': 15, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 678 Chain: "G" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 1452 Classifications: {'peptide': 363} Incomplete info: {'backbone_only': 338} Link IDs: {'PTRANS': 15, 'TRANS': 347} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1435 Unresolved non-hydrogen angles: 2074 Unresolved non-hydrogen dihedrals: 915 Unresolved non-hydrogen chiralities: 445 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 26, 'TYR:plan': 11, 'GLN:plan1': 10, 'ASP:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 628 Chain: "H" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 1524 Classifications: {'peptide': 381} Incomplete info: {'backbone_only': 357} Link IDs: {'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1504 Unresolved non-hydrogen angles: 2173 Unresolved non-hydrogen dihedrals: 954 Unresolved non-hydrogen chiralities: 466 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 13, 'ASP:plan': 14, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 666 Chain: "I" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 1552 Classifications: {'peptide': 388} Incomplete info: {'backbone_only': 362} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1523 Unresolved non-hydrogen angles: 2202 Unresolved non-hydrogen dihedrals: 963 Unresolved non-hydrogen chiralities: 473 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 14, 'ASP:plan': 15, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 678 Chain: "J" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 1572 Classifications: {'peptide': 393} Incomplete info: {'backbone_only': 366} Link IDs: {'PTRANS': 15, 'TRANS': 377} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1537 Unresolved non-hydrogen angles: 2222 Unresolved non-hydrogen dihedrals: 971 Unresolved non-hydrogen chiralities: 479 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 29, 'TYR:plan': 11, 'GLN:plan1': 13, 'ASP:plan': 15, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 679 Chain: "K" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 1560 Classifications: {'peptide': 390} Incomplete info: {'backbone_only': 363} Link IDs: {'PTRANS': 15, 'TRANS': 374} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1532 Unresolved non-hydrogen angles: 2213 Unresolved non-hydrogen dihedrals: 970 Unresolved non-hydrogen chiralities: 475 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 29, 'TYR:plan': 11, 'GLN:plan1': 13, 'ASP:plan': 15, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 679 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 1500 Classifications: {'peptide': 375} Incomplete info: {'backbone_only': 351} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1483 Unresolved non-hydrogen angles: 2142 Unresolved non-hydrogen dihedrals: 941 Unresolved non-hydrogen chiralities: 460 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 12, 'ASP:plan': 14, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 652 Chain: "M" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 1464 Classifications: {'peptide': 366} Incomplete info: {'backbone_only': 342} Link IDs: {'PTRANS': 15, 'TRANS': 350} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1456 Unresolved non-hydrogen angles: 2101 Unresolved non-hydrogen dihedrals: 928 Unresolved non-hydrogen chiralities: 449 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 640 Chain: "N" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 1460 Classifications: {'peptide': 365} Incomplete info: {'backbone_only': 340} Link IDs: {'PTRANS': 15, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1447 Unresolved non-hydrogen angles: 2090 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 447 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 27, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 637 Chain: "O" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 1456 Classifications: {'peptide': 364} Incomplete info: {'backbone_only': 340} Link IDs: {'PTRANS': 15, 'TRANS': 348} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1442 Unresolved non-hydrogen angles: 2082 Unresolved non-hydrogen dihedrals: 917 Unresolved non-hydrogen chiralities: 447 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 27, 'TYR:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 629 Chain: "X" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 960 Classifications: {'RNA': 48} Modifications used: {'rna2p_pyr': 11, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 36} Chain: "Z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 840 Classifications: {'RNA': 42} Modifications used: {'rna2p_pyr': 11, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 31} Time building chain proxies: 7.30, per 1000 atoms: 0.30 Number of scatterers: 24128 At special positions: 0 Unit cell: (169.776, 179.208, 204.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 90 15.00 O 6302 8.00 N 5762 7.00 C 11974 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 317 helices and 15 sheets defined 69.3% alpha, 3.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.732A pdb=" N THR A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.553A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 157 through 180 removed outlier: 4.183A pdb=" N LEU A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.839A pdb=" N ARG A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.595A pdb=" N ASN A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 285 through 305 removed outlier: 4.072A pdb=" N SER A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Proline residue: A 309 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 311' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.585A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.528A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.582A pdb=" N PHE A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.529A pdb=" N GLY B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 106 through 110 removed outlier: 4.196A pdb=" N GLY B 110 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 139 Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 157 through 180 removed outlier: 4.199A pdb=" N LEU B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 177 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.505A pdb=" N LYS B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 224 through 240 removed outlier: 3.832A pdb=" N ARG B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.584A pdb=" N ASN B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 279 through 286 removed outlier: 6.052A pdb=" N ASN B 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B 286 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 305 Processing helix chain 'B' and resid 306 through 311 Proline residue: B 309 - end of helix No H-bonds generated for 'chain 'B' and resid 306 through 311' Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.506A pdb=" N THR B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.531A pdb=" N GLY C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 157 through 180 removed outlier: 4.147A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 177 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 210 through 224 Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.849A pdb=" N ARG C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.554A pdb=" N ASN C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'C' and resid 279 through 286 removed outlier: 6.056A pdb=" N ASN C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU C 286 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 305 Processing helix chain 'C' and resid 306 through 311 Proline residue: C 309 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 311' Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.554A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.506A pdb=" N THR C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.674A pdb=" N HIS C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 18 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.535A pdb=" N GLY D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 121 through 139 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 157 through 180 removed outlier: 4.137A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA D 177 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 224 Processing helix chain 'D' and resid 224 through 240 removed outlier: 3.851A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.592A pdb=" N ASN D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'D' and resid 279 through 286 removed outlier: 6.050A pdb=" N ASN D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU D 286 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 Processing helix chain 'D' and resid 306 through 311 Proline residue: D 309 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 311' Processing helix chain 'D' and resid 317 through 323 removed outlier: 4.300A pdb=" N LYS D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.513A pdb=" N THR D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.693A pdb=" N HIS D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.537A pdb=" N GLY E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 121 through 139 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 157 through 180 removed outlier: 4.162A pdb=" N LEU E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA E 177 " --> pdb=" O TRP E 173 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL E 180 " --> pdb=" O ILE E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 224 through 240 removed outlier: 3.847A pdb=" N ARG E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 3.590A pdb=" N ASN E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 removed outlier: 3.511A pdb=" N ILE E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.838A pdb=" N ALA E 283 " --> pdb=" O PRO E 280 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN E 285 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 305 removed outlier: 4.463A pdb=" N ASP E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 318 through 323 Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.514A pdb=" N THR E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 369 Processing helix chain 'E' and resid 373 through 377 Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 44 through 61 removed outlier: 4.567A pdb=" N GLU F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.537A pdb=" N GLY F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'F' and resid 123 through 139 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 157 through 180 removed outlier: 4.128A pdb=" N LEU F 175 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA F 177 " --> pdb=" O TRP F 173 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL F 180 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 224 through 240 removed outlier: 3.838A pdb=" N ARG F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 240 " --> pdb=" O ILE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 3.636A pdb=" N ASN F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'F' and resid 284 through 305 removed outlier: 3.714A pdb=" N SER F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN F 292 " --> pdb=" O GLN F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 Proline residue: F 309 - end of helix No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 317 through 323 removed outlier: 4.102A pdb=" N LYS F 321 " --> pdb=" O SER F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 326 No H-bonds generated for 'chain 'F' and resid 324 through 326' Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.530A pdb=" N THR F 340 " --> pdb=" O GLY F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 369 Processing helix chain 'F' and resid 387 through 397 removed outlier: 3.840A pdb=" N ALA F 393 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 44 through 61 Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.507A pdb=" N GLY G 71 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 124 through 139 Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 157 through 180 removed outlier: 4.144A pdb=" N LEU G 175 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA G 177 " --> pdb=" O TRP G 173 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 200 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 210 through 224 Processing helix chain 'G' and resid 224 through 240 removed outlier: 3.836A pdb=" N ARG G 228 " --> pdb=" O SER G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.601A pdb=" N ASN G 257 " --> pdb=" O SER G 253 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 287 through 305 Processing helix chain 'G' and resid 306 through 311 Proline residue: G 309 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 311' Processing helix chain 'G' and resid 318 through 323 Processing helix chain 'G' and resid 324 through 326 No H-bonds generated for 'chain 'G' and resid 324 through 326' Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.513A pdb=" N THR G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 369 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 44 through 61 removed outlier: 3.681A pdb=" N ARG H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.530A pdb=" N GLY H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 121 through 139 Processing helix chain 'H' and resid 148 through 153 Processing helix chain 'H' and resid 157 through 180 removed outlier: 4.151A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA H 177 " --> pdb=" O TRP H 173 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL H 180 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 200 Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 210 through 224 Processing helix chain 'H' and resid 224 through 240 removed outlier: 3.905A pdb=" N ARG H 228 " --> pdb=" O SER H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 3.617A pdb=" N ASN H 257 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR H 258 " --> pdb=" O ASP H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 removed outlier: 3.514A pdb=" N ILE H 271 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 removed outlier: 6.019A pdb=" N ASN H 285 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU H 286 " --> pdb=" O ALA H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 305 Processing helix chain 'H' and resid 306 through 311 Proline residue: H 309 - end of helix No H-bonds generated for 'chain 'H' and resid 306 through 311' Processing helix chain 'H' and resid 318 through 323 removed outlier: 3.566A pdb=" N PHE H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 326 No H-bonds generated for 'chain 'H' and resid 324 through 326' Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.540A pdb=" N THR H 340 " --> pdb=" O GLY H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 369 removed outlier: 3.722A pdb=" N HIS H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 394 Processing helix chain 'I' and resid 5 through 18 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 65 through 77 removed outlier: 3.564A pdb=" N GLY I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'I' and resid 120 through 139 removed outlier: 3.879A pdb=" N GLU I 124 " --> pdb=" O LYS I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 153 Processing helix chain 'I' and resid 157 through 180 removed outlier: 4.196A pdb=" N LEU I 175 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA I 177 " --> pdb=" O TRP I 173 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS I 178 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL I 180 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 200 removed outlier: 4.657A pdb=" N SER I 189 " --> pdb=" O THR I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 Processing helix chain 'I' and resid 210 through 224 Processing helix chain 'I' and resid 224 through 240 removed outlier: 3.897A pdb=" N ARG I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS I 240 " --> pdb=" O ILE I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 260 removed outlier: 3.620A pdb=" N ASN I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'I' and resid 279 through 286 removed outlier: 6.001A pdb=" N ASN I 285 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 305 Processing helix chain 'I' and resid 306 through 311 Proline residue: I 309 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 311' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.554A pdb=" N PHE I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 326 No H-bonds generated for 'chain 'I' and resid 324 through 326' Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.510A pdb=" N THR I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 370 removed outlier: 3.777A pdb=" N ALA I 367 " --> pdb=" O GLY I 363 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG I 368 " --> pdb=" O GLN I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 390 through 397 Processing helix chain 'J' and resid 5 through 18 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 44 through 61 Processing helix chain 'J' and resid 65 through 77 removed outlier: 3.564A pdb=" N GLY J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'J' and resid 122 through 139 removed outlier: 3.922A pdb=" N GLU J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 157 through 180 removed outlier: 4.139A pdb=" N LEU J 175 " --> pdb=" O GLN J 171 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE J 176 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA J 177 " --> pdb=" O TRP J 173 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL J 180 " --> pdb=" O ILE J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 200 Processing helix chain 'J' and resid 204 through 208 Processing helix chain 'J' and resid 210 through 224 Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.867A pdb=" N ARG J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 240 " --> pdb=" O ILE J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.588A pdb=" N ASN J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'J' and resid 279 through 285 removed outlier: 5.402A pdb=" N ASN J 285 " --> pdb=" O LEU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 305 removed outlier: 3.570A pdb=" N ASP J 290 " --> pdb=" O GLU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 311 Proline residue: J 309 - end of helix No H-bonds generated for 'chain 'J' and resid 306 through 311' Processing helix chain 'J' and resid 318 through 323 removed outlier: 3.541A pdb=" N PHE J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 342 removed outlier: 3.677A pdb=" N SER J 332 " --> pdb=" O PRO J 328 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET J 335 " --> pdb=" O TRP J 331 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 369 Processing helix chain 'J' and resid 388 through 396 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 25 through 29 Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.538A pdb=" N GLY K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 92 Processing helix chain 'K' and resid 122 through 139 removed outlier: 3.504A pdb=" N GLU K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'K' and resid 157 through 180 removed outlier: 4.134A pdb=" N LEU K 175 " --> pdb=" O GLN K 171 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE K 176 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL K 180 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 200 Processing helix chain 'K' and resid 204 through 208 Processing helix chain 'K' and resid 210 through 224 Processing helix chain 'K' and resid 224 through 240 removed outlier: 3.853A pdb=" N ARG K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 260 removed outlier: 3.602A pdb=" N ASN K 257 " --> pdb=" O SER K 253 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR K 258 " --> pdb=" O ASP K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'K' and resid 279 through 286 removed outlier: 4.151A pdb=" N ALA K 283 " --> pdb=" O PRO K 280 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN K 285 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU K 286 " --> pdb=" O ALA K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 Processing helix chain 'K' and resid 306 through 311 Proline residue: K 309 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 311' Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.143A pdb=" N LYS K 321 " --> pdb=" O SER K 317 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.526A pdb=" N THR K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 369 Processing helix chain 'K' and resid 386 through 393 Processing helix chain 'L' and resid 5 through 18 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 44 through 61 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.516A pdb=" N GLY L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 Processing helix chain 'L' and resid 122 through 139 Processing helix chain 'L' and resid 148 through 153 Processing helix chain 'L' and resid 157 through 180 removed outlier: 4.130A pdb=" N LEU L 175 " --> pdb=" O GLN L 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA L 177 " --> pdb=" O TRP L 173 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS L 178 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL L 180 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 200 Processing helix chain 'L' and resid 204 through 208 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.843A pdb=" N ARG L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 260 removed outlier: 3.564A pdb=" N ILE L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN L 257 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR L 258 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'L' and resid 279 through 286 removed outlier: 6.035A pdb=" N ASN L 285 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU L 286 " --> pdb=" O ALA L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 305 Processing helix chain 'L' and resid 306 through 311 Proline residue: L 309 - end of helix No H-bonds generated for 'chain 'L' and resid 306 through 311' Processing helix chain 'L' and resid 318 through 323 Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.529A pdb=" N THR L 340 " --> pdb=" O GLY L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 368 Processing helix chain 'L' and resid 387 through 393 Processing helix chain 'M' and resid 5 through 18 Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 44 through 61 Processing helix chain 'M' and resid 65 through 77 removed outlier: 3.512A pdb=" N GLY M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 92 Processing helix chain 'M' and resid 120 through 139 removed outlier: 3.838A pdb=" N GLU M 124 " --> pdb=" O LYS M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 153 Processing helix chain 'M' and resid 157 through 180 removed outlier: 4.127A pdb=" N LEU M 175 " --> pdb=" O GLN M 171 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE M 176 " --> pdb=" O ILE M 172 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA M 177 " --> pdb=" O TRP M 173 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS M 178 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 200 Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 210 through 224 Processing helix chain 'M' and resid 224 through 240 removed outlier: 3.768A pdb=" N ARG M 228 " --> pdb=" O SER M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 260 removed outlier: 3.605A pdb=" N ASN M 257 " --> pdb=" O SER M 253 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR M 258 " --> pdb=" O ASP M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 273 Processing helix chain 'M' and resid 279 through 284 Processing helix chain 'M' and resid 287 through 305 Processing helix chain 'M' and resid 307 through 311 removed outlier: 3.542A pdb=" N MET M 311 " --> pdb=" O ALA M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 323 removed outlier: 4.088A pdb=" N LYS M 321 " --> pdb=" O SER M 317 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE M 322 " --> pdb=" O ILE M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 326 No H-bonds generated for 'chain 'M' and resid 324 through 326' Processing helix chain 'M' and resid 327 through 342 Processing helix chain 'M' and resid 356 through 369 removed outlier: 3.927A pdb=" N HIS M 369 " --> pdb=" O LYS M 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 18 Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 44 through 61 removed outlier: 3.603A pdb=" N GLU N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.513A pdb=" N GLY N 71 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 Processing helix chain 'N' and resid 123 through 139 Processing helix chain 'N' and resid 148 through 153 Processing helix chain 'N' and resid 157 through 180 removed outlier: 4.070A pdb=" N LEU N 175 " --> pdb=" O GLN N 171 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE N 176 " --> pdb=" O ILE N 172 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA N 177 " --> pdb=" O TRP N 173 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS N 178 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL N 180 " --> pdb=" O ILE N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 200 removed outlier: 3.528A pdb=" N LYS N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 208 Processing helix chain 'N' and resid 210 through 224 Processing helix chain 'N' and resid 224 through 240 removed outlier: 3.666A pdb=" N ARG N 228 " --> pdb=" O SER N 224 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS N 240 " --> pdb=" O ILE N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 260 removed outlier: 4.320A pdb=" N TYR N 258 " --> pdb=" O ASP N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 273 Processing helix chain 'N' and resid 279 through 283 removed outlier: 3.538A pdb=" N LEU N 282 " --> pdb=" O TYR N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 286 No H-bonds generated for 'chain 'N' and resid 284 through 286' Processing helix chain 'N' and resid 287 through 305 Processing helix chain 'N' and resid 306 through 311 Proline residue: N 309 - end of helix No H-bonds generated for 'chain 'N' and resid 306 through 311' Processing helix chain 'N' and resid 318 through 323 removed outlier: 3.540A pdb=" N PHE N 322 " --> pdb=" O ILE N 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 342 removed outlier: 3.509A pdb=" N THR N 340 " --> pdb=" O GLY N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 356 through 369 removed outlier: 3.505A pdb=" N ALA N 367 " --> pdb=" O GLY N 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 18 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'O' and resid 44 through 61 Processing helix chain 'O' and resid 65 through 77 removed outlier: 3.531A pdb=" N GLY O 71 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 92 Processing helix chain 'O' and resid 122 through 139 Processing helix chain 'O' and resid 148 through 153 Processing helix chain 'O' and resid 157 through 177 removed outlier: 3.555A pdb=" N THR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU O 175 " --> pdb=" O GLN O 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA O 177 " --> pdb=" O TRP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 200 removed outlier: 3.666A pdb=" N LYS O 196 " --> pdb=" O ARG O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 210 through 224 Processing helix chain 'O' and resid 224 through 240 removed outlier: 3.659A pdb=" N ARG O 228 " --> pdb=" O SER O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 260 removed outlier: 3.571A pdb=" N ASN O 257 " --> pdb=" O SER O 253 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR O 258 " --> pdb=" O ASP O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 273 Processing helix chain 'O' and resid 279 through 286 removed outlier: 3.636A pdb=" N ALA O 283 " --> pdb=" O PRO O 280 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN O 285 " --> pdb=" O LEU O 282 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU O 286 " --> pdb=" O ALA O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 305 Processing helix chain 'O' and resid 306 through 311 Proline residue: O 309 - end of helix No H-bonds generated for 'chain 'O' and resid 306 through 311' Processing helix chain 'O' and resid 318 through 323 removed outlier: 3.582A pdb=" N PHE O 322 " --> pdb=" O ILE O 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 326 No H-bonds generated for 'chain 'O' and resid 324 through 326' Processing helix chain 'O' and resid 327 through 342 removed outlier: 3.501A pdb=" N THR O 340 " --> pdb=" O GLY O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 367 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.012A pdb=" N THR A 33 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 100 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 35 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 37 " --> pdb=" O ILE A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.762A pdb=" N THR B 33 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 100 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 35 " --> pdb=" O VAL B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 39 Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 40 removed outlier: 3.723A pdb=" N VAL D 104 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 33 through 38 removed outlier: 6.013A pdb=" N THR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL E 100 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE E 35 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE E 102 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 37 " --> pdb=" O ILE E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AA7, first strand: chain 'G' and resid 33 through 38 removed outlier: 5.950A pdb=" N THR G 33 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL G 100 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE G 37 " --> pdb=" O ILE G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 33 through 40 removed outlier: 5.868A pdb=" N THR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL H 100 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE H 102 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE H 37 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL H 104 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL H 39 " --> pdb=" O VAL H 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 33 through 39 Processing sheet with id=AB1, first strand: chain 'J' and resid 33 through 40 removed outlier: 5.884A pdb=" N THR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL J 100 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE J 35 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE J 102 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE J 37 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL J 104 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL J 39 " --> pdb=" O VAL J 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 33 through 40 removed outlier: 6.037A pdb=" N THR K 33 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL K 100 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE K 35 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE K 37 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL K 104 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL K 39 " --> pdb=" O VAL K 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 39 removed outlier: 5.889A pdb=" N THR L 33 " --> pdb=" O GLU L 98 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL L 100 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE L 35 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE L 37 " --> pdb=" O ILE L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 33 through 40 Processing sheet with id=AB5, first strand: chain 'N' and resid 33 through 39 removed outlier: 6.028A pdb=" N THR N 33 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL N 100 " --> pdb=" O THR N 33 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE N 35 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE N 102 " --> pdb=" O ILE N 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE N 37 " --> pdb=" O ILE N 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 33 through 40 2442 hydrogen bonds defined for protein. 7014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.28: 5751 1.28 - 1.37: 5685 1.37 - 1.47: 6006 1.47 - 1.57: 6668 1.57 - 1.67: 171 Bond restraints: 24281 Sorted by residual: bond pdb=" O5' U X 1 " pdb=" C5' U X 1 " ideal model delta sigma weight residual 1.420 1.499 -0.079 1.50e-02 4.44e+03 2.75e+01 bond pdb=" C TRP D 194 " pdb=" O TRP D 194 " ideal model delta sigma weight residual 1.236 1.297 -0.060 1.15e-02 7.56e+03 2.73e+01 bond pdb=" C THR N 33 " pdb=" O THR N 33 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.22e-02 6.72e+03 2.29e+01 bond pdb=" C GLN L 364 " pdb=" O GLN L 364 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 bond pdb=" C VAL C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.03e+01 ... (remaining 24276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 29640 4.43 - 8.86: 1207 8.86 - 13.29: 34 13.29 - 17.72: 5 17.72 - 22.15: 1 Bond angle restraints: 30887 Sorted by residual: angle pdb=" C4' U X 36 " pdb=" C3' U X 36 " pdb=" O3' U X 36 " ideal model delta sigma weight residual 109.40 87.25 22.15 1.50e+00 4.44e-01 2.18e+02 angle pdb=" C4' U Z 18 " pdb=" C3' U Z 18 " pdb=" O3' U Z 18 " ideal model delta sigma weight residual 113.00 97.85 15.15 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C GLY O 110 " pdb=" N ILE O 111 " pdb=" CA ILE O 111 " ideal model delta sigma weight residual 120.33 127.97 -7.64 8.00e-01 1.56e+00 9.13e+01 angle pdb=" C GLY I 110 " pdb=" N ILE I 111 " pdb=" CA ILE I 111 " ideal model delta sigma weight residual 120.33 127.07 -6.74 8.00e-01 1.56e+00 7.11e+01 angle pdb=" C LYS I 245 " pdb=" N GLY I 246 " pdb=" CA GLY I 246 " ideal model delta sigma weight residual 120.60 128.12 -7.52 1.01e+00 9.80e-01 5.55e+01 ... (remaining 30882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 5982 12.66 - 25.32: 634 25.32 - 37.97: 188 37.97 - 50.63: 85 50.63 - 63.29: 102 Dihedral angle restraints: 6991 sinusoidal: 1434 harmonic: 5557 Sorted by residual: dihedral pdb=" CA GLY O 246 " pdb=" C GLY O 246 " pdb=" N ARG O 247 " pdb=" CA ARG O 247 " ideal model delta harmonic sigma weight residual -180.00 -130.20 -49.80 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA LYS O 240 " pdb=" C LYS O 240 " pdb=" N GLY O 241 " pdb=" CA GLY O 241 " ideal model delta harmonic sigma weight residual -180.00 -137.25 -42.75 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA ASP O 147 " pdb=" C ASP O 147 " pdb=" N SER O 148 " pdb=" CA SER O 148 " ideal model delta harmonic sigma weight residual -180.00 -137.99 -42.01 0 5.00e+00 4.00e-02 7.06e+01 ... (remaining 6988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 447 0.390 - 0.780: 2 0.780 - 1.170: 0 1.170 - 1.560: 0 1.560 - 1.950: 1 Chirality restraints: 450 Sorted by residual: chirality pdb=" P U Z 1 " pdb=" OP1 U Z 1 " pdb=" OP2 U Z 1 " pdb=" O5' U Z 1 " both_signs ideal model delta sigma weight residual True 2.41 0.46 1.95 2.00e-01 2.50e+01 9.50e+01 chirality pdb=" C3' U Z 27 " pdb=" C4' U Z 27 " pdb=" O3' U Z 27 " pdb=" C2' U Z 27 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C2' U X 34 " pdb=" C3' U X 34 " pdb=" O2' U X 34 " pdb=" C1' U X 34 " both_signs ideal model delta sigma weight residual False -2.75 -2.29 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 447 not shown) Planarity restraints: 5647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U X 9 " -0.077 2.00e-02 2.50e+03 4.11e-02 3.80e+01 pdb=" N1 U X 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U X 9 " 0.022 2.00e-02 2.50e+03 pdb=" O2 U X 9 " 0.023 2.00e-02 2.50e+03 pdb=" N3 U X 9 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U X 9 " -0.042 2.00e-02 2.50e+03 pdb=" O4 U X 9 " -0.041 2.00e-02 2.50e+03 pdb=" C5 U X 9 " 0.059 2.00e-02 2.50e+03 pdb=" C6 U X 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 267 " 0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C PHE B 267 " -0.095 2.00e-02 2.50e+03 pdb=" O PHE B 267 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE B 268 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 332 " -0.027 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C SER D 332 " 0.095 2.00e-02 2.50e+03 pdb=" O SER D 332 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE D 333 " -0.031 2.00e-02 2.50e+03 ... (remaining 5644 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 349 2.68 - 3.23: 24964 3.23 - 3.79: 28527 3.79 - 4.34: 35888 4.34 - 4.90: 52332 Nonbonded interactions: 142060 Sorted by model distance: nonbonded pdb=" N GLY N 325 " pdb=" N GLY N 326 " model vdw 2.119 2.560 nonbonded pdb=" N GLY A 325 " pdb=" N GLY A 326 " model vdw 2.166 2.560 nonbonded pdb=" O THR F 181 " pdb=" O2' U Z 32 " model vdw 2.342 3.040 nonbonded pdb=" O THR O 181 " pdb=" O2 U X 44 " model vdw 2.352 3.040 nonbonded pdb=" N PRO E 324 " pdb=" O PRO E 324 " model vdw 2.397 2.496 ... (remaining 142055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'B' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'C' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'D' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'E' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'F' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'G' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'H' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'I' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'L' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'M' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'N' and (resid 32 through 114 or resid 123 through 367)) selection = (chain 'O' and (resid 32 through 114 or resid 123 through 367)) } ncs_group { reference = (chain 'J' and resid 4 through 393) selection = chain 'K' } ncs_group { reference = (chain 'X' and resid 7 through 48) selection = chain 'Z' } 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.570 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.012 0.079 24281 Z= 0.951 Angle : 2.068 22.149 30887 Z= 1.557 Chirality : 0.147 1.950 450 Planarity : 0.010 0.055 5647 Dihedral : 12.205 63.287 6991 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.03 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.56 % Twisted General : 0.51 % 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: -2.44 (0.10), residues: 5532 helix: -1.56 (0.07), residues: 3342 sheet: -0.55 (0.27), residues: 198 loop : -1.53 (0.13), residues: 1992 Details of bonding type rmsd covalent geometry : bond 0.01246 (24281) covalent geometry : angle 2.06752 (30887) hydrogen bonds : bond 0.19439 ( 2442) hydrogen bonds : angle 7.09382 ( 7014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.835 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0960 time to fit residues: 43.1888 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 50.0000 chunk 223 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038501 restraints weight = 283165.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038905 restraints weight = 234798.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039167 restraints weight = 200903.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039460 restraints weight = 179073.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.039622 restraints weight = 163024.233| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24281 Z= 0.160 Angle : 0.489 7.240 30887 Z= 0.309 Chirality : 0.037 0.174 450 Planarity : 0.003 0.017 5647 Dihedral : 10.761 87.879 6991 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.10 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 1.06 (0.11), residues: 5532 helix: 1.46 (0.09), residues: 3424 sheet: -0.16 (0.30), residues: 208 loop : -0.51 (0.14), residues: 1900 Details of bonding type rmsd covalent geometry : bond 0.00216 (24281) covalent geometry : angle 0.48949 (30887) hydrogen bonds : bond 0.03741 ( 2442) hydrogen bonds : angle 4.22041 ( 7014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.966 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1036 time to fit residues: 46.8182 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 31 optimal weight: 0.0020 chunk 490 optimal weight: 50.0000 chunk 240 optimal weight: 4.9990 chunk 335 optimal weight: 0.9980 chunk 448 optimal weight: 30.0000 chunk 379 optimal weight: 50.0000 chunk 150 optimal weight: 40.0000 chunk 433 optimal weight: 5.9990 chunk 122 optimal weight: 0.0010 chunk 556 optimal weight: 30.0000 chunk 529 optimal weight: 0.3980 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.039809 restraints weight = 278176.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040204 restraints weight = 229413.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.040567 restraints weight = 196692.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.040785 restraints weight = 174710.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041041 restraints weight = 159378.743| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 24281 Z= 0.075 Angle : 0.342 4.576 30887 Z= 0.214 Chirality : 0.033 0.180 450 Planarity : 0.002 0.016 5647 Dihedral : 10.024 76.072 6991 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.54 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.64 (0.12), residues: 5532 helix: 2.72 (0.09), residues: 3455 sheet: 0.67 (0.32), residues: 190 loop : 0.02 (0.15), residues: 1887 Details of bonding type rmsd covalent geometry : bond 0.00103 (24281) covalent geometry : angle 0.34223 (30887) hydrogen bonds : bond 0.02392 ( 2442) hydrogen bonds : angle 3.30239 ( 7014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.911 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1034 time to fit residues: 46.3065 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 156 optimal weight: 9.9990 chunk 390 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 238 optimal weight: 40.0000 chunk 529 optimal weight: 8.9990 chunk 120 optimal weight: 50.0000 chunk 199 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 334 optimal weight: 40.0000 chunk 415 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038443 restraints weight = 285826.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.038835 restraints weight = 234512.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039189 restraints weight = 199685.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039395 restraints weight = 176941.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.039636 restraints weight = 160897.159| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 24281 Z= 0.156 Angle : 0.410 5.158 30887 Z= 0.262 Chirality : 0.040 0.168 450 Planarity : 0.002 0.020 5647 Dihedral : 10.409 87.354 6991 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.57 (0.12), residues: 5532 helix: 2.74 (0.09), residues: 3463 sheet: 0.39 (0.30), residues: 228 loop : -0.18 (0.15), residues: 1841 Details of bonding type rmsd covalent geometry : bond 0.00214 (24281) covalent geometry : angle 0.41036 (30887) hydrogen bonds : bond 0.03226 ( 2442) hydrogen bonds : angle 3.81001 ( 7014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1018 time to fit residues: 45.2093 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 295 optimal weight: 30.0000 chunk 438 optimal weight: 20.0000 chunk 374 optimal weight: 2.9990 chunk 195 optimal weight: 40.0000 chunk 100 optimal weight: 1.9990 chunk 507 optimal weight: 40.0000 chunk 335 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 359 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039026 restraints weight = 281254.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.039417 restraints weight = 230214.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039788 restraints weight = 196108.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.040010 restraints weight = 173123.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040255 restraints weight = 156845.544| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 24281 Z= 0.107 Angle : 0.350 4.970 30887 Z= 0.220 Chirality : 0.042 0.198 450 Planarity : 0.002 0.021 5647 Dihedral : 10.382 86.410 6991 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.82 (0.12), residues: 5532 helix: 2.95 (0.09), residues: 3472 sheet: 0.45 (0.31), residues: 224 loop : -0.11 (0.15), residues: 1836 Details of bonding type rmsd covalent geometry : bond 0.00149 (24281) covalent geometry : angle 0.34959 (30887) hydrogen bonds : bond 0.02384 ( 2442) hydrogen bonds : angle 3.46182 ( 7014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1048 time to fit residues: 47.3519 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 413 optimal weight: 20.0000 chunk 33 optimal weight: 50.0000 chunk 298 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 346 optimal weight: 0.2980 chunk 274 optimal weight: 7.9990 chunk 28 optimal weight: 50.0000 chunk 358 optimal weight: 50.0000 chunk 278 optimal weight: 40.0000 chunk 360 optimal weight: 30.0000 chunk 352 optimal weight: 50.0000 overall best weight: 7.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038460 restraints weight = 286472.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.038885 restraints weight = 233131.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039171 restraints weight = 198074.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.039478 restraints weight = 175214.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039643 restraints weight = 158109.698| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 24281 Z= 0.158 Angle : 0.414 5.731 30887 Z= 0.265 Chirality : 0.047 0.310 450 Planarity : 0.002 0.021 5647 Dihedral : 11.040 94.667 6991 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.43 (0.12), residues: 5532 helix: 2.70 (0.09), residues: 3468 sheet: 0.02 (0.32), residues: 206 loop : -0.34 (0.15), residues: 1858 Details of bonding type rmsd covalent geometry : bond 0.00219 (24281) covalent geometry : angle 0.41379 (30887) hydrogen bonds : bond 0.03117 ( 2442) hydrogen bonds : angle 3.92924 ( 7014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0956 time to fit residues: 43.1594 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 419 optimal weight: 40.0000 chunk 152 optimal weight: 30.0000 chunk 461 optimal weight: 0.0170 chunk 62 optimal weight: 0.0170 chunk 466 optimal weight: 30.0000 chunk 119 optimal weight: 0.0170 chunk 188 optimal weight: 50.0000 chunk 395 optimal weight: 40.0000 chunk 287 optimal weight: 50.0000 chunk 159 optimal weight: 30.0000 chunk 387 optimal weight: 0.0670 overall best weight: 6.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038896 restraints weight = 285479.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039287 restraints weight = 232113.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.039683 restraints weight = 197204.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039912 restraints weight = 172654.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040168 restraints weight = 156061.895| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 24281 Z= 0.121 Angle : 0.361 5.685 30887 Z= 0.230 Chirality : 0.045 0.280 450 Planarity : 0.002 0.019 5647 Dihedral : 11.004 97.793 6991 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.66 (0.12), residues: 5532 helix: 2.92 (0.09), residues: 3476 sheet: 0.00 (0.34), residues: 192 loop : -0.34 (0.15), residues: 1864 Details of bonding type rmsd covalent geometry : bond 0.00169 (24281) covalent geometry : angle 0.36115 (30887) hydrogen bonds : bond 0.02576 ( 2442) hydrogen bonds : angle 3.61919 ( 7014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.840 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1064 time to fit residues: 47.9173 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 511 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 528 optimal weight: 50.0000 chunk 155 optimal weight: 5.9990 chunk 28 optimal weight: 50.0000 chunk 520 optimal weight: 40.0000 chunk 461 optimal weight: 7.9990 chunk 232 optimal weight: 30.0000 chunk 553 optimal weight: 20.0000 chunk 543 optimal weight: 50.0000 chunk 346 optimal weight: 0.0370 overall best weight: 10.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038104 restraints weight = 289814.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038527 restraints weight = 235408.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.038855 restraints weight = 200709.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039060 restraints weight = 176581.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.039319 restraints weight = 160062.142| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 24281 Z= 0.217 Angle : 0.479 6.721 30887 Z= 0.306 Chirality : 0.054 0.332 450 Planarity : 0.003 0.020 5647 Dihedral : 11.505 105.780 6991 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.02 (0.12), residues: 5532 helix: 2.48 (0.09), residues: 3443 sheet: -0.33 (0.36), residues: 182 loop : -0.67 (0.14), residues: 1907 Details of bonding type rmsd covalent geometry : bond 0.00304 (24281) covalent geometry : angle 0.47854 (30887) hydrogen bonds : bond 0.03639 ( 2442) hydrogen bonds : angle 4.37361 ( 7014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.872 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1071 time to fit residues: 48.3987 Evaluate side-chains 231 residues out of total 4631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 56.1755 > 50: distance: 4 - 17: 3.787 distance: 12 - 25: 8.626 distance: 16 - 29: 7.285 distance: 18 - 19: 3.675 distance: 19 - 20: 4.797 distance: 20 - 33: 13.257 distance: 21 - 22: 6.424 distance: 22 - 23: 8.284 distance: 23 - 24: 12.301 distance: 23 - 25: 13.078 distance: 25 - 26: 6.839 distance: 26 - 27: 11.618 distance: 27 - 28: 10.495 distance: 27 - 29: 12.212 distance: 29 - 30: 14.447 distance: 30 - 31: 7.584 distance: 31 - 32: 16.095 distance: 31 - 33: 16.862 distance: 33 - 34: 15.979 distance: 34 - 35: 46.798 distance: 35 - 36: 56.175 distance: 35 - 37: 31.422 distance: 37 - 38: 13.222 distance: 38 - 39: 9.493 distance: 39 - 40: 33.946 distance: 39 - 41: 8.029 distance: 41 - 42: 9.642 distance: 42 - 43: 18.757 distance: 43 - 44: 12.904 distance: 43 - 45: 14.560 distance: 45 - 46: 35.331 distance: 46 - 47: 7.959 distance: 47 - 48: 23.536 distance: 47 - 49: 20.791 distance: 49 - 50: 10.275 distance: 50 - 51: 36.657 distance: 51 - 52: 17.453 distance: 51 - 53: 19.174 distance: 53 - 54: 55.827 distance: 54 - 55: 28.282 distance: 55 - 56: 10.708 distance: 55 - 57: 17.642