Starting phenix.real_space_refine on Sun Sep 13 14:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_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_12584/09_2026/7nt6_12584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nt6_12584/09_2026/7nt6_12584.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 42} Modifications used: {'rna2p_pyr': 11, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 31} Time building chain proxies: 6.20, per 1000 atoms: 0.26 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.39 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: 4.61 Time building geometry restraints manager: 2.95 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=" 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=" O3' U Z 27 " pdb=" P U Z 28 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.53e+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=" O3' U Z 18 " pdb=" P U Z 19 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.20e-02 6.94e+03 2.22e+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 ... (remaining 24276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 30150 5.05 - 10.10: 720 10.10 - 15.15: 14 15.15 - 20.20: 2 20.20 - 25.25: 1 Bond angle restraints: 30887 Sorted by residual: 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=" C4' U X 36 " pdb=" C3' U X 36 " pdb=" O3' U X 36 " ideal model delta sigma weight residual 112.50 87.25 25.25 3.00e+00 1.11e-01 7.08e+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 angle pdb=" N PRO E 324 " pdb=" CA PRO E 324 " pdb=" C PRO E 324 " ideal model delta sigma weight residual 111.57 100.30 11.27 1.52e+00 4.33e-01 5.49e+01 ... (remaining 30882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5972 15.67 - 31.33: 438 31.33 - 46.99: 122 46.99 - 62.66: 71 62.66 - 78.32: 28 Dihedral angle restraints: 6631 sinusoidal: 1074 harmonic: 5557 Sorted by residual: dihedral pdb=" C4' U Z 36 " pdb=" C3' U Z 36 " pdb=" C2' U Z 36 " pdb=" C1' U Z 36 " ideal model delta sinusoidal sigma weight residual 36.34 -41.97 78.32 1 3.10e+00 1.04e-01 7.97e+02 dihedral pdb=" C4' U X 24 " pdb=" C3' U X 24 " pdb=" C2' U X 24 " pdb=" C1' U X 24 " ideal model delta sinusoidal sigma weight residual 36.35 -39.18 75.52 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' U Z 6 " pdb=" C3' U Z 6 " pdb=" C2' U Z 6 " pdb=" C1' U Z 6 " ideal model delta sinusoidal sigma weight residual 36.34 -37.32 73.67 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 6628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 445 0.343 - 0.685: 4 0.685 - 1.028: 0 1.028 - 1.370: 0 1.370 - 1.713: 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 2.17 0.46 1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" C3' U X 36 " pdb=" C4' U X 36 " pdb=" O3' U X 36 " pdb=" C2' U X 36 " both_signs ideal model delta sigma weight residual False -2.50 -3.01 0.51 2.00e-01 2.50e+01 6.61e+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 -2.79 -2.29 -0.50 2.00e-01 2.50e+01 6.19e+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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.470 Find NCS groups from input model: 0.870 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.074 24281 Z= 0.947 Angle : 2.068 25.249 30887 Z= 1.526 Chirality : 0.165 1.713 450 Planarity : 0.010 0.055 5647 Dihedral : 11.892 78.319 6631 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 are 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/Z covalent geometry : bond 0.01245 / 0.95 (24281) covalent geometry : angle 2.06791 / 1.53 (30887) hydrogen bonds : bond 0.19439 / 15.18 ( 2442) hydrogen bonds : angle 7.09382 / 5.85 ( 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 : 1.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0991 time to fit residues: 44.8231 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 : 0.852 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038461 restraints weight = 281115.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.038813 restraints weight = 231827.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039171 restraints weight = 199212.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.039364 restraints weight = 177446.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.039563 restraints weight = 162972.003| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24281 Z= 0.169 Angle : 0.735 18.015 30887 Z= 0.353 Chirality : 0.136 0.789 450 Planarity : 0.003 0.015 5647 Dihedral : 10.286 147.911 6631 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.07 % 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 are not related in a simple way. whole: 0.95 (0.11), residues: 5532 helix: 1.35 (0.09), residues: 3443 sheet: -0.10 (0.30), residues: 206 loop : -0.55 (0.14), residues: 1883 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.17 (24281) covalent geometry : angle 0.73471 / 0.35 (30887) hydrogen bonds : bond 0.04054 / 3.19 ( 2442) hydrogen bonds : angle 4.23926 / 3.51 ( 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 : 0.974 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1033 time to fit residues: 46.6807 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 : 0.918 ------------------------------------------------------------------------------- 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: 40.0000 chunk 490 optimal weight: 50.0000 chunk 240 optimal weight: 7.9990 chunk 335 optimal weight: 9.9990 chunk 448 optimal weight: 1.9990 chunk 379 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 433 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 556 optimal weight: 20.0000 chunk 529 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039335 restraints weight = 279144.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039754 restraints weight = 230309.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.040031 restraints weight = 197269.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.040339 restraints weight = 175161.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.040531 restraints weight = 159549.130| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.021 24281 Z= 0.093 Angle : 0.510 10.595 30887 Z= 0.247 Chirality : 0.095 0.432 450 Planarity : 0.002 0.013 5647 Dihedral : 9.583 158.392 6631 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % 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 are not related in a simple way. whole: 2.45 (0.12), residues: 5532 helix: 2.58 (0.09), residues: 3460 sheet: 0.39 (0.30), residues: 218 loop : -0.07 (0.15), residues: 1854 Details of bonding type rmsd/Z covalent geometry : bond 0.00141 / 0.09 (24281) covalent geometry : angle 0.50968 / 0.25 (30887) hydrogen bonds : bond 0.02521 / 1.99 ( 2442) hydrogen bonds : angle 3.46986 / 2.86 ( 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 : 0.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1039 time to fit residues: 46.7191 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 : 0.957 ------------------------------------------------------------------------------- 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: 10.0000 chunk 390 optimal weight: 9.9990 chunk 150 optimal weight: 40.0000 chunk 238 optimal weight: 40.0000 chunk 529 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 334 optimal weight: 40.0000 chunk 415 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038078 restraints weight = 288466.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038477 restraints weight = 235601.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038786 restraints weight = 202127.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.038991 restraints weight = 178863.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039248 restraints weight = 162673.650| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24281 Z= 0.187 Angle : 0.670 12.217 30887 Z= 0.322 Chirality : 0.124 0.423 450 Planarity : 0.003 0.014 5647 Dihedral : 9.790 144.510 6631 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % 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 are not related in a simple way. whole: 2.20 (0.12), residues: 5532 helix: 2.48 (0.09), residues: 3439 sheet: 0.15 (0.30), residues: 218 loop : -0.34 (0.15), residues: 1875 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.19 (24281) covalent geometry : angle 0.66955 / 0.32 (30887) hydrogen bonds : bond 0.03562 / 2.81 ( 2442) hydrogen bonds : angle 4.14385 / 3.42 ( 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 : 0.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0997 time to fit residues: 45.1548 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 : 0.827 ------------------------------------------------------------------------------- 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: 5.9990 chunk 195 optimal weight: 40.0000 chunk 100 optimal weight: 20.0000 chunk 507 optimal weight: 40.0000 chunk 335 optimal weight: 0.2980 chunk 328 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 359 optimal weight: 40.0000 overall best weight: 9.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.038161 restraints weight = 288247.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038583 restraints weight = 235206.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.038914 restraints weight = 200326.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039172 restraints weight = 176402.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.039342 restraints weight = 159596.150| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 24281 Z= 0.184 Angle : 0.684 14.012 30887 Z= 0.316 Chirality : 0.140 0.792 450 Planarity : 0.002 0.018 5647 Dihedral : 9.617 142.447 6631 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % 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 are not related in a simple way. whole: 2.14 (0.12), residues: 5532 helix: 2.49 (0.09), residues: 3457 sheet: -0.37 (0.31), residues: 200 loop : -0.45 (0.15), residues: 1875 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.18 (24281) covalent geometry : angle 0.68377 / 0.32 (30887) hydrogen bonds : bond 0.03249 / 2.56 ( 2442) hydrogen bonds : angle 4.11335 / 3.39 ( 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 : 1.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1070 time to fit residues: 48.4254 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 : 0.962 ------------------------------------------------------------------------------- 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: 40.0000 chunk 298 optimal weight: 30.0000 chunk 414 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 28 optimal weight: 50.0000 chunk 358 optimal weight: 40.0000 chunk 278 optimal weight: 40.0000 chunk 360 optimal weight: 0.0470 chunk 352 optimal weight: 50.0000 overall best weight: 7.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038395 restraints weight = 287380.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038821 restraints weight = 234301.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039103 restraints weight = 199273.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039408 restraints weight = 176496.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039624 restraints weight = 159497.757| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24281 Z= 0.153 Angle : 0.660 14.081 30887 Z= 0.293 Chirality : 0.134 0.766 450 Planarity : 0.002 0.017 5647 Dihedral : 9.392 137.879 6631 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.81 % 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 are not related in a simple way. whole: 2.24 (0.12), residues: 5532 helix: 2.62 (0.09), residues: 3456 sheet: -0.41 (0.34), residues: 186 loop : -0.53 (0.15), residues: 1890 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.15 (24281) covalent geometry : angle 0.65968 / 0.29 (30887) hydrogen bonds : bond 0.02947 / 2.32 ( 2442) hydrogen bonds : angle 3.98162 / 3.27 ( 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 : 1.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1055 time to fit residues: 47.7448 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 : 0.970 ------------------------------------------------------------------------------- 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: 8.9990 chunk 461 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 466 optimal weight: 30.0000 chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 50.0000 chunk 395 optimal weight: 30.0000 chunk 287 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 387 optimal weight: 6.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038293 restraints weight = 288907.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.038719 restraints weight = 235248.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.039062 restraints weight = 199889.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039281 restraints weight = 175357.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039521 restraints weight = 159526.247| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24281 Z= 0.171 Angle : 0.690 14.241 30887 Z= 0.309 Chirality : 0.134 0.771 450 Planarity : 0.002 0.019 5647 Dihedral : 9.461 138.408 6631 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % 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 are not related in a simple way. whole: 2.09 (0.12), residues: 5532 helix: 2.55 (0.09), residues: 3450 sheet: -0.62 (0.35), residues: 186 loop : -0.64 (0.15), residues: 1896 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.17 (24281) covalent geometry : angle 0.69020 / 0.31 (30887) hydrogen bonds : bond 0.03122 / 2.46 ( 2442) hydrogen bonds : angle 4.08585 / 3.36 ( 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 : 0.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1058 time to fit residues: 47.9137 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 : 0.950 ------------------------------------------------------------------------------- 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: 30.0000 chunk 146 optimal weight: 10.0000 chunk 528 optimal weight: 50.0000 chunk 155 optimal weight: 0.2980 chunk 28 optimal weight: 50.0000 chunk 520 optimal weight: 50.0000 chunk 461 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 553 optimal weight: 10.0000 chunk 543 optimal weight: 50.0000 chunk 346 optimal weight: 4.9990 overall best weight: 7.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038544 restraints weight = 286770.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038966 restraints weight = 234456.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039261 restraints weight = 198678.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039570 restraints weight = 175023.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039734 restraints weight = 157459.244| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.002 0.022 24281 Z= 0.149 Angle : 0.665 14.604 30887 Z= 0.290 Chirality : 0.131 0.735 450 Planarity : 0.002 0.019 5647 Dihedral : 9.309 137.883 6631 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % 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 are not related in a simple way. whole: 2.28 (0.12), residues: 5532 helix: 2.71 (0.09), residues: 3452 sheet: -0.43 (0.38), residues: 170 loop : -0.63 (0.15), residues: 1910 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.15 (24281) covalent geometry : angle 0.66497 / 0.29 (30887) hydrogen bonds : bond 0.02854 / 2.25 ( 2442) hydrogen bonds : angle 3.95991 / 3.25 ( 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 : 0.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1034 time to fit residues: 46.7026 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 : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 27 optimal weight: 50.0000 chunk 514 optimal weight: 50.0000 chunk 116 optimal weight: 9.9990 chunk 431 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 402 optimal weight: 7.9990 chunk 345 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 174 optimal weight: 50.0000 chunk 327 optimal weight: 10.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039010 restraints weight = 330700.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039279 restraints weight = 282274.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.039516 restraints weight = 247665.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039719 restraints weight = 222704.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039835 restraints weight = 205928.753| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24281 Z= 0.274 Angle : 0.856 15.430 30887 Z= 0.398 Chirality : 0.153 0.847 450 Planarity : 0.003 0.021 5647 Dihedral : 9.925 138.786 6631 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.98 % Favored : 93.00 % 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 are not related in a simple way. whole: 1.21 (0.12), residues: 5532 helix: 1.97 (0.09), residues: 3406 sheet: -1.14 (0.41), residues: 138 loop : -1.16 (0.14), residues: 1988 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.27 (24281) covalent geometry : angle 0.85598 / 0.40 (30887) hydrogen bonds : bond 0.04238 / 3.34 ( 2442) hydrogen bonds : angle 4.97507 / 4.09 ( 7014) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.960 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1030 time to fit residues: 46.7025 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 : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 413 optimal weight: 40.0000 chunk 287 optimal weight: 0.0050 chunk 166 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 280 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 220 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 chunk 125 optimal weight: 50.0000 chunk 517 optimal weight: 10.0000 overall best weight: 4.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.038743 restraints weight = 285434.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.039149 restraints weight = 231117.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039543 restraints weight = 195278.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.039818 restraints weight = 171262.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039996 restraints weight = 154113.456| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24281 Z= 0.109 Angle : 0.670 14.502 30887 Z= 0.282 Chirality : 0.132 0.644 450 Planarity : 0.002 0.019 5647 Dihedral : 9.302 138.993 6631 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % 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 are not related in a simple way. whole: 2.18 (0.12), residues: 5532 helix: 2.73 (0.09), residues: 3443 sheet: -0.72 (0.41), residues: 154 loop : -0.82 (0.14), residues: 1935 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.11 (24281) covalent geometry : angle 0.66992 / 0.28 (30887) hydrogen bonds : bond 0.02624 / 2.07 ( 2442) hydrogen bonds : angle 3.96339 / 3.25 ( 7014) ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.932 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1040 time to fit residues: 46.8901 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 : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 239 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 171 optimal weight: 0.5980 chunk 284 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 317 optimal weight: 30.0000 chunk 406 optimal weight: 50.0000 chunk 218 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 510 optimal weight: 50.0000 chunk 555 optimal weight: 10.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.038651 restraints weight = 285501.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039086 restraints weight = 231195.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.039382 restraints weight = 196538.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039685 restraints weight = 173232.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039865 restraints weight = 156053.804| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24281 Z= 0.135 Angle : 0.691 14.329 30887 Z= 0.292 Chirality : 0.131 0.638 450 Planarity : 0.002 0.019 5647 Dihedral : 9.308 138.718 6631 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.69 % Favored : 94.29 % 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 are not related in a simple way. whole: 2.26 (0.12), residues: 5532 helix: 2.80 (0.09), residues: 3446 sheet: -0.53 (0.45), residues: 134 loop : -0.84 (0.14), residues: 1952 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.14 (24281) covalent geometry : angle 0.69147 / 0.29 (30887) hydrogen bonds : bond 0.02774 / 2.19 ( 2442) hydrogen bonds : angle 3.98696 / 3.28 ( 7014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.27 seconds wall clock time: 68 minutes 26.35 seconds (4106.35 seconds total)