Starting phenix.real_space_refine on Tue Mar 19 12:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_12584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_12584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_12584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_12584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt6_12584/03_2024/7nt6_12584.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 10, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 11, 'PHE:plan': 14, 'GLU:plan': 25, 'ARG:plan': 22} 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: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 26, 'ARG:plan': 26} 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: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28} 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: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28} 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: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28} 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: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 29, 'ARG:plan': 28} 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: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 26} 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: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 14, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28} 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: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28} 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: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 29} 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: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 29} 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: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 14, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28} 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: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 28} 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: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 27} 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: {'GLN:plan1': 11, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 629 Chain: "X" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 960 Classifications: {'RNA': 48} Modifications used: {'rna2p_pyr': 11, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 36} Chain: "Z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 840 Classifications: {'RNA': 42} Modifications used: {'rna2p_pyr': 11, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 31} Time building chain proxies: 13.52, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 10.69 Conformation dependent library (CDL) restraints added in 6.7 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: 7.24 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: 9.57 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.28: 5751 1.28 - 1.37: 5685 1.37 - 1.47: 6006 1.47 - 1.57: 6668 1.57 - 1.67: 171 Bond restraints: 24281 Sorted by residual: bond pdb=" O5' U X 1 " pdb=" C5' U X 1 " ideal model delta sigma weight residual 1.420 1.499 -0.079 1.50e-02 4.44e+03 2.75e+01 bond pdb=" C TRP D 194 " pdb=" O TRP D 194 " ideal model delta sigma weight residual 1.236 1.297 -0.060 1.15e-02 7.56e+03 2.73e+01 bond pdb=" C THR N 33 " pdb=" O THR N 33 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.22e-02 6.72e+03 2.29e+01 bond pdb=" C GLN L 364 " pdb=" O GLN L 364 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 bond pdb=" C VAL C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.03e+01 ... (remaining 24276 not shown) Histogram of bond angle deviations from ideal: 87.25 - 96.53: 4 96.53 - 105.80: 418 105.80 - 115.07: 7407 115.07 - 124.35: 20585 124.35 - 133.62: 2473 Bond angle restraints: 30887 Sorted by residual: angle pdb=" C4' U X 36 " pdb=" C3' U X 36 " pdb=" O3' U X 36 " ideal model delta sigma weight residual 109.40 87.25 22.15 1.50e+00 4.44e-01 2.18e+02 angle pdb=" C4' U Z 18 " pdb=" C3' U Z 18 " pdb=" O3' U Z 18 " ideal model delta sigma weight residual 113.00 97.85 15.15 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C GLY O 110 " pdb=" N ILE O 111 " pdb=" CA ILE O 111 " ideal model delta sigma weight residual 120.33 127.97 -7.64 8.00e-01 1.56e+00 9.13e+01 angle pdb=" C GLY I 110 " pdb=" N ILE I 111 " pdb=" CA ILE I 111 " ideal model delta sigma weight residual 120.33 127.07 -6.74 8.00e-01 1.56e+00 7.11e+01 angle pdb=" C LYS I 245 " pdb=" N GLY I 246 " pdb=" CA GLY I 246 " ideal model delta sigma weight residual 120.60 128.12 -7.52 1.01e+00 9.80e-01 5.55e+01 ... (remaining 30882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 5982 12.66 - 25.32: 634 25.32 - 37.97: 188 37.97 - 50.63: 85 50.63 - 63.29: 102 Dihedral angle restraints: 6991 sinusoidal: 1434 harmonic: 5557 Sorted by residual: dihedral pdb=" CA GLY O 246 " pdb=" C GLY O 246 " pdb=" N ARG O 247 " pdb=" CA ARG O 247 " ideal model delta harmonic sigma weight residual -180.00 -130.20 -49.80 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA LYS O 240 " pdb=" C LYS O 240 " pdb=" N GLY O 241 " pdb=" CA GLY O 241 " ideal model delta harmonic sigma weight residual -180.00 -137.25 -42.75 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA ASP O 147 " pdb=" C ASP O 147 " pdb=" N SER O 148 " pdb=" CA SER O 148 " ideal model delta harmonic sigma weight residual -180.00 -137.99 -42.01 0 5.00e+00 4.00e-02 7.06e+01 ... (remaining 6988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 447 0.390 - 0.780: 2 0.780 - 1.170: 0 1.170 - 1.560: 0 1.560 - 1.950: 1 Chirality restraints: 450 Sorted by residual: chirality pdb=" P U Z 1 " pdb=" OP1 U Z 1 " pdb=" OP2 U Z 1 " pdb=" O5' U Z 1 " both_signs ideal model delta sigma weight residual True 2.41 0.46 1.95 2.00e-01 2.50e+01 9.50e+01 chirality pdb=" C3' U Z 27 " pdb=" C4' U Z 27 " pdb=" O3' U Z 27 " pdb=" C2' U Z 27 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C2' U X 34 " pdb=" C3' U X 34 " pdb=" O2' U X 34 " pdb=" C1' U X 34 " both_signs ideal model delta sigma weight residual False -2.75 -2.29 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 447 not shown) Planarity restraints: 5647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U X 9 " -0.077 2.00e-02 2.50e+03 4.11e-02 3.80e+01 pdb=" N1 U X 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U X 9 " 0.022 2.00e-02 2.50e+03 pdb=" O2 U X 9 " 0.023 2.00e-02 2.50e+03 pdb=" N3 U X 9 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U X 9 " -0.042 2.00e-02 2.50e+03 pdb=" O4 U X 9 " -0.041 2.00e-02 2.50e+03 pdb=" C5 U X 9 " 0.059 2.00e-02 2.50e+03 pdb=" C6 U X 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 267 " 0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C PHE B 267 " -0.095 2.00e-02 2.50e+03 pdb=" O PHE B 267 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE B 268 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 332 " -0.027 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C SER D 332 " 0.095 2.00e-02 2.50e+03 pdb=" O SER D 332 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE D 333 " -0.031 2.00e-02 2.50e+03 ... (remaining 5644 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 349 2.68 - 3.23: 24964 3.23 - 3.79: 28527 3.79 - 4.34: 35888 4.34 - 4.90: 52332 Nonbonded interactions: 142060 Sorted by model distance: nonbonded pdb=" N GLY N 325 " pdb=" N GLY N 326 " model vdw 2.119 2.560 nonbonded pdb=" N GLY A 325 " pdb=" N GLY A 326 " model vdw 2.166 2.560 nonbonded pdb=" O THR F 181 " pdb=" O2' U Z 32 " model vdw 2.342 2.440 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 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: 0.010 Normalize map: mean=0, sd=1: 0.690 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: 3.360 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 73.030 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.079 24281 Z= 0.931 Angle : 2.068 22.149 30887 Z= 1.557 Chirality : 0.147 1.950 450 Planarity : 0.010 0.055 5647 Dihedral : 12.205 63.287 6991 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.03 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.56 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1923 time to fit residues: 87.9597 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 472 optimal weight: 7.9990 chunk 424 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 286 optimal weight: 50.0000 chunk 226 optimal weight: 8.9990 chunk 438 optimal weight: 0.3980 chunk 169 optimal weight: 0.0270 chunk 266 optimal weight: 0.0060 chunk 326 optimal weight: 7.9990 chunk 508 optimal weight: 20.0000 overall best weight: 1.8456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2194 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= 0.110 Angle : 0.445 6.634 30887 Z= 0.278 Chirality : 0.033 0.203 450 Planarity : 0.002 0.015 5647 Dihedral : 10.605 87.209 6991 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.11), residues: 5532 helix: 1.74 (0.09), residues: 3410 sheet: 0.07 (0.31), residues: 192 loop : -0.38 (0.14), residues: 1930 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1959 time to fit residues: 90.2107 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 282 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 423 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 509 optimal weight: 0.0070 chunk 550 optimal weight: 50.0000 chunk 453 optimal weight: 40.0000 chunk 505 optimal weight: 50.0000 chunk 173 optimal weight: 20.0000 chunk 408 optimal weight: 4.9990 overall best weight: 7.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24281 Z= 0.163 Angle : 0.452 6.200 30887 Z= 0.287 Chirality : 0.043 0.204 450 Planarity : 0.002 0.019 5647 Dihedral : 10.531 84.379 6991 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.12), residues: 5532 helix: 2.47 (0.09), residues: 3468 sheet: -0.03 (0.29), residues: 232 loop : -0.33 (0.15), residues: 1832 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.802 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2044 time to fit residues: 94.7601 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 503 optimal weight: 30.0000 chunk 383 optimal weight: 20.0000 chunk 264 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 243 optimal weight: 40.0000 chunk 342 optimal weight: 40.0000 chunk 511 optimal weight: 20.0000 chunk 541 optimal weight: 40.0000 chunk 267 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24281 Z= 0.288 Angle : 0.620 7.484 30887 Z= 0.397 Chirality : 0.062 0.334 450 Planarity : 0.004 0.023 5647 Dihedral : 11.798 94.456 6991 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5532 helix: 1.59 (0.09), residues: 3409 sheet: -0.92 (0.31), residues: 186 loop : -0.98 (0.14), residues: 1937 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.919 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1997 time to fit residues: 93.1916 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 450 optimal weight: 0.0770 chunk 307 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 403 optimal weight: 40.0000 chunk 223 optimal weight: 30.0000 chunk 461 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 276 optimal weight: 0.0770 chunk 485 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 overall best weight: 12.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 24281 Z= 0.240 Angle : 0.524 8.228 30887 Z= 0.337 Chirality : 0.059 0.363 450 Planarity : 0.003 0.023 5647 Dihedral : 11.709 94.795 6991 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.00 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.12), residues: 5532 helix: 1.82 (0.09), residues: 3414 sheet: -0.89 (0.34), residues: 186 loop : -1.04 (0.14), residues: 1932 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.769 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1945 time to fit residues: 89.4279 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 182 optimal weight: 0.0970 chunk 487 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 317 optimal weight: 30.0000 chunk 133 optimal weight: 1.9990 chunk 541 optimal weight: 50.0000 chunk 449 optimal weight: 20.0000 chunk 250 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 179 optimal weight: 30.0000 chunk 284 optimal weight: 8.9990 overall best weight: 12.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 24281 Z= 0.245 Angle : 0.541 7.608 30887 Z= 0.345 Chirality : 0.060 0.362 450 Planarity : 0.003 0.024 5647 Dihedral : 12.102 100.013 6991 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.56 % Favored : 92.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 5532 helix: 1.69 (0.09), residues: 3397 sheet: -1.30 (0.38), residues: 159 loop : -1.20 (0.14), residues: 1976 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.130 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2043 time to fit residues: 93.5636 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 522 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 308 optimal weight: 6.9990 chunk 395 optimal weight: 40.0000 chunk 306 optimal weight: 40.0000 chunk 456 optimal weight: 50.0000 chunk 302 optimal weight: 0.0010 chunk 539 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 329 optimal weight: 30.0000 chunk 249 optimal weight: 50.0000 overall best weight: 13.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 24281 Z= 0.265 Angle : 0.562 8.967 30887 Z= 0.360 Chirality : 0.062 0.355 450 Planarity : 0.003 0.022 5647 Dihedral : 12.269 102.634 6991 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.11), residues: 5532 helix: 1.62 (0.09), residues: 3355 sheet: -1.20 (0.43), residues: 136 loop : -1.39 (0.14), residues: 2041 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.850 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2025 time to fit residues: 92.9502 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 333 optimal weight: 0.7980 chunk 215 optimal weight: 40.0000 chunk 322 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 104 optimal weight: 30.0000 chunk 343 optimal weight: 8.9990 chunk 367 optimal weight: 0.0770 chunk 266 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 overall best weight: 2.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 24281 Z= 0.086 Angle : 0.368 6.984 30887 Z= 0.233 Chirality : 0.048 0.278 450 Planarity : 0.002 0.022 5647 Dihedral : 11.673 106.350 6991 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.12), residues: 5532 helix: 2.72 (0.09), residues: 3388 sheet: -1.03 (0.39), residues: 170 loop : -0.98 (0.14), residues: 1974 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1982 time to fit residues: 90.2565 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 490 optimal weight: 50.0000 chunk 517 optimal weight: 30.0000 chunk 471 optimal weight: 50.0000 chunk 502 optimal weight: 50.0000 chunk 516 optimal weight: 30.0000 chunk 302 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 394 optimal weight: 0.6980 chunk 154 optimal weight: 0.4980 chunk 454 optimal weight: 0.7980 chunk 475 optimal weight: 0.0980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 24281 Z= 0.070 Angle : 0.304 5.408 30887 Z= 0.194 Chirality : 0.040 0.236 450 Planarity : 0.001 0.018 5647 Dihedral : 11.422 107.489 6991 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.12), residues: 5532 helix: 3.28 (0.09), residues: 3416 sheet: -0.85 (0.43), residues: 144 loop : -0.67 (0.15), residues: 1972 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.813 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2004 time to fit residues: 91.8341 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 501 optimal weight: 50.0000 chunk 330 optimal weight: 8.9990 chunk 531 optimal weight: 50.0000 chunk 324 optimal weight: 8.9990 chunk 252 optimal weight: 50.0000 chunk 369 optimal weight: 50.0000 chunk 557 optimal weight: 20.0000 chunk 513 optimal weight: 30.0000 chunk 444 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 343 optimal weight: 0.9980 overall best weight: 7.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 24281 Z= 0.171 Angle : 0.400 6.125 30887 Z= 0.258 Chirality : 0.045 0.240 450 Planarity : 0.002 0.018 5647 Dihedral : 11.821 104.517 6991 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.12), residues: 5532 helix: 3.07 (0.09), residues: 3422 sheet: -0.77 (0.43), residues: 152 loop : -0.89 (0.14), residues: 1958 ********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.528 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1933 time to fit residues: 87.9869 Evaluate side-chains 231 residues out of total 4631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 272 optimal weight: 0.1980 chunk 352 optimal weight: 30.0000 chunk 473 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 409 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 444 optimal weight: 30.0000 chunk 186 optimal weight: 30.0000 chunk 456 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 overall best weight: 15.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039151 restraints weight = 331340.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.039438 restraints weight = 281903.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.039632 restraints weight = 248228.607| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 24281 Z= 0.301 Angle : 0.590 7.673 30887 Z= 0.379 Chirality : 0.060 0.255 450 Planarity : 0.004 0.019 5647 Dihedral : 12.445 117.203 6991 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.33 % Favored : 91.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 5532 helix: 1.89 (0.09), residues: 3401 sheet: -0.93 (0.46), residues: 131 loop : -1.40 (0.14), residues: 2000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.54 seconds wall clock time: 64 minutes 56.14 seconds (3896.14 seconds total)