Starting phenix.real_space_refine on Sun Feb 8 09:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.map" model { file = "/net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msg_48588/02_2026/9msg_48588.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 2 5.21 5 S 145 5.16 5 C 26814 2.51 5 N 7436 2.21 5 O 8383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42869 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "B" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "D" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "F" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1964 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2368 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1351, 10513 Classifications: {'peptide': 1351} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1295} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3599 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "U" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "V" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MG': 1, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27085 SG CYS J 70 53.604 71.538 129.690 1.00 50.34 S ATOM 27099 SG CYS J 72 55.433 72.242 132.859 1.00 60.68 S ATOM 27207 SG CYS J 85 52.037 73.490 132.749 1.00 54.86 S ATOM 27231 SG CYS J 88 54.907 75.180 130.720 1.00 51.95 S ATOM 32919 SG CYS J 814 36.312 100.545 68.807 1.00 53.66 S ATOM 33484 SG CYS J 888 39.605 99.875 70.796 1.00 51.31 S ATOM 33535 SG CYS J 895 37.875 97.177 68.910 1.00 44.19 S ATOM 33556 SG CYS J 898 39.523 99.725 67.041 1.00 54.54 S Time building chain proxies: 9.03, per 1000 atoms: 0.21 Number of scatterers: 42869 At special positions: 0 Unit cell: (163.4, 172.86, 239.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 87 15.00 Mg 2 11.99 O 8383 8.00 N 7436 7.00 C 26814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb=" ZN J1504 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 888 " Number of angles added : 12 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9710 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 71 sheets defined 45.1% alpha, 14.1% beta 33 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.549A pdb=" N LEU A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 309 through 315 removed outlier: 4.425A pdb=" N LYS A 314 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A 315 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.650A pdb=" N LEU A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.677A pdb=" N LEU A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.524A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.642A pdb=" N LEU B 243 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.609A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.701A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.507A pdb=" N TYR B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 333 removed outlier: 4.264A pdb=" N ARG B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 354 through 369 Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.077A pdb=" N LEU B 380 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 removed outlier: 3.593A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 Processing helix chain 'C' and resid 203 through 210 removed outlier: 3.550A pdb=" N GLY C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.629A pdb=" N ALA C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 316 through 332 removed outlier: 4.171A pdb=" N ARG C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 354 through 369 removed outlier: 3.530A pdb=" N GLU C 358 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 172 through 184 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.523A pdb=" N GLU D 242 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.978A pdb=" N ILE D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.712A pdb=" N TYR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 313 through 333 removed outlier: 3.648A pdb=" N ILE D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Proline residue: D 319 - end of helix Processing helix chain 'D' and resid 340 through 348 Processing helix chain 'D' and resid 354 through 369 Processing helix chain 'E' and resid 143 through 157 Processing helix chain 'E' and resid 172 through 184 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 251 through 257 removed outlier: 4.014A pdb=" N ILE E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 289 Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 317 through 332 Processing helix chain 'E' and resid 340 through 350 Processing helix chain 'E' and resid 354 through 369 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 172 through 184 Processing helix chain 'F' and resid 203 through 209 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.596A pdb=" N GLU F 242 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 251 through 258 removed outlier: 3.551A pdb=" N SER F 257 " --> pdb=" O ARG F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 309 through 315 removed outlier: 5.089A pdb=" N LYS F 314 " --> pdb=" O ARG F 311 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU F 315 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 333 Processing helix chain 'F' and resid 343 through 350 removed outlier: 3.841A pdb=" N LEU F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 370 removed outlier: 3.588A pdb=" N GLU F 358 " --> pdb=" O GLY F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 4.001A pdb=" N LEU F 380 " --> pdb=" O ASP F 376 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.591A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.447A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 283 removed outlier: 3.908A pdb=" N GLN G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 292 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.678A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.696A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.551A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.555A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 55 removed outlier: 3.620A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.829A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.633A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 3.742A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.986A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 478 removed outlier: 3.603A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.557A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.762A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.517A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.116A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 907 through 912 removed outlier: 4.272A pdb=" N SER I 911 " --> pdb=" O GLY I 907 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.765A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 986 through 992 removed outlier: 3.628A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.210A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.572A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.803A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.757A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.795A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 10 Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.776A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.722A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.502A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 4.379A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.569A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.869A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.615A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.121A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.585A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.880A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.546A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.720A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 removed outlier: 3.562A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.911A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 removed outlier: 3.526A pdb=" N LEU J 840 " --> pdb=" O ARG J 836 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.568A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 Processing helix chain 'J' and resid 1136 through 1147 removed outlier: 3.820A pdb=" N ARG J1140 " --> pdb=" O GLY J1136 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.571A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.544A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.503A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.607A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.624A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.636A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1374 removed outlier: 3.538A pdb=" N ALA J1374 " --> pdb=" O MET J1370 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 79 Processing helix chain 'M' and resid 23 through 28 removed outlier: 4.399A pdb=" N GLN M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 23 through 28' Processing helix chain 'M' and resid 29 through 44 Processing helix chain 'M' and resid 68 through 75 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.508A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.548A pdb=" N ILE M 161 " --> pdb=" O PRO M 157 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 4.244A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.709A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.758A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 255 Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.649A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 312 through 351 Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.743A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 400 through 403 Processing helix chain 'M' and resid 417 through 429 Processing helix chain 'M' and resid 438 through 448 Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 5.963A pdb=" N LEU A 235 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA A 278 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 237 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 163 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR A 279 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE A 165 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 305 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 307 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.299A pdb=" N GLY A 338 " --> pdb=" O ILE A 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 195 removed outlier: 6.110A pdb=" N LEU B 235 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA B 278 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 237 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 163 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR B 279 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 165 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 195 removed outlier: 6.547A pdb=" N VAL C 192 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 238 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 194 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU C 235 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA C 278 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 237 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.527A pdb=" N PHE C 260 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 269 " --> pdb=" O PHE C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.777A pdb=" N GLY C 338 " --> pdb=" O ILE C 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 191 through 195 removed outlier: 6.874A pdb=" N VAL D 192 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP D 238 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 194 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 235 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA D 278 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 237 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 163 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR D 279 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 165 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB3, first strand: chain 'D' and resid 259 through 260 Processing sheet with id=AB4, first strand: chain 'E' and resid 191 through 195 Processing sheet with id=AB5, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB6, first strand: chain 'E' and resid 338 through 339 removed outlier: 7.269A pdb=" N GLY E 338 " --> pdb=" O ILE E 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 191 through 195 removed outlier: 6.185A pdb=" N LEU F 235 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA F 278 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU F 237 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 163 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR F 279 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE F 165 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 261 Processing sheet with id=AC1, first strand: chain 'F' and resid 338 through 339 removed outlier: 7.242A pdb=" N GLY F 338 " --> pdb=" O ILE F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 12 through 20 removed outlier: 6.895A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.524A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.539A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.507A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 97 through 105 removed outlier: 8.122A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AD1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AD2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.533A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.364A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AD6, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.527A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.863A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 228 through 231 Processing sheet with id=AD9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AE1, first strand: chain 'I' and resid 249 through 250 removed outlier: 4.466A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.979A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.880A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.092A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AE6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.567A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.726A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AE9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AF1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.074A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.884A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AF4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.789A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 1244 through 1245 Processing sheet with id=AF6, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.774A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.566A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.198A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.095A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 315 through 317 removed outlier: 3.600A pdb=" N GLU M 54 " --> pdb=" O THR J 317 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AG3, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AG4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AG5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AG6, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.817A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.617A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.080A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.898A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 1035 through 1038 Processing sheet with id=AH2, first strand: chain 'J' and resid 1046 through 1048 Processing sheet with id=AH3, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.388A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.574A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.349A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AH7, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.552A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 406 through 409 1750 hydrogen bonds defined for protein. 4902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 11.97 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12446 1.33 - 1.45: 6377 1.45 - 1.57: 24426 1.57 - 1.69: 164 1.69 - 1.81: 240 Bond restraints: 43653 Sorted by residual: bond pdb=" O POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 1.661 1.607 0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" O POP J1501 " pdb=" P1 POP J1501 " ideal model delta sigma weight residual 1.660 1.608 0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" C ASP J1184 " pdb=" N PRO J1185 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.77e+00 bond pdb=" O2 POP J1501 " pdb=" P1 POP J1501 " ideal model delta sigma weight residual 1.531 1.507 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CA GLY J 173 " pdb=" C GLY J 173 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.39e+00 ... (remaining 43648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 59160 3.77 - 7.54: 47 7.54 - 11.31: 0 11.31 - 15.07: 0 15.07 - 18.84: 1 Bond angle restraints: 59208 Sorted by residual: angle pdb=" P1 POP J1501 " pdb=" O POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 139.66 120.82 18.84 3.00e+00 1.11e-01 3.95e+01 angle pdb=" C ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.02e+01 angle pdb=" C ASN E 355 " pdb=" CA ASN E 355 " pdb=" CB ASN E 355 " ideal model delta sigma weight residual 116.34 109.96 6.38 1.40e+00 5.10e-01 2.08e+01 angle pdb=" N VAL E 220 " pdb=" CA VAL E 220 " pdb=" C VAL E 220 " ideal model delta sigma weight residual 113.71 109.59 4.12 9.50e-01 1.11e+00 1.88e+01 angle pdb=" CA ASN B 355 " pdb=" C ASN B 355 " pdb=" N VAL B 356 " ideal model delta sigma weight residual 119.63 116.34 3.29 8.10e-01 1.52e+00 1.65e+01 ... (remaining 59203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 25011 17.96 - 35.91: 1283 35.91 - 53.87: 375 53.87 - 71.82: 89 71.82 - 89.78: 9 Dihedral angle restraints: 26767 sinusoidal: 11697 harmonic: 15070 Sorted by residual: dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU J 701 " pdb=" C LEU J 701 " pdb=" N GLN J 702 " pdb=" CA GLN J 702 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 26764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4524 0.033 - 0.066: 1558 0.066 - 0.100: 390 0.100 - 0.133: 220 0.133 - 0.166: 16 Chirality restraints: 6708 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE I 734 " pdb=" N ILE I 734 " pdb=" C ILE I 734 " pdb=" CB ILE I 734 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 6705 not shown) Planarity restraints: 7426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 212 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO H 213 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 213 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 213 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO I 698 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO J 359 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " 0.020 5.00e-02 4.00e+02 ... (remaining 7423 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 571 2.67 - 3.23: 38207 3.23 - 3.78: 62911 3.78 - 4.34: 89150 4.34 - 4.90: 146673 Nonbonded interactions: 337512 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1502 " model vdw 2.110 2.170 nonbonded pdb=" OG SER M 382 " pdb=" OP2 DT U 45 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.191 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR M 461 " pdb=" OP1 DG V 52 " model vdw 2.223 3.040 ... (remaining 337507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'B' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'C' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'D' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'E' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'F' and resid 139 through 384) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 47.450 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.260 43661 Z= 0.132 Angle : 0.469 18.843 59220 Z= 0.256 Chirality : 0.040 0.166 6708 Planarity : 0.003 0.041 7426 Dihedral : 12.205 89.778 17057 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.56 % Allowed : 3.59 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5199 helix: 1.50 (0.12), residues: 2061 sheet: 1.06 (0.21), residues: 610 loop : -0.50 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I1301 TYR 0.015 0.001 TYR J 631 PHE 0.013 0.001 PHE J1319 TRP 0.005 0.001 TRP J 686 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00249 (43653) covalent geometry : angle 0.46895 (59208) hydrogen bonds : bond 0.15508 ( 1825) hydrogen bonds : angle 5.65031 ( 5056) metal coordination : bond 0.13790 ( 8) metal coordination : angle 0.03119 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.1486 (mmm) cc_final: 0.0235 (ttt) REVERT: D 251 LEU cc_start: 0.2247 (OUTLIER) cc_final: 0.0954 (mt) REVERT: F 150 LEU cc_start: -0.0430 (OUTLIER) cc_final: -0.0725 (tp) REVERT: F 335 GLU cc_start: 0.3489 (mt-10) cc_final: 0.2611 (tt0) REVERT: G 228 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8304 (mp) REVERT: I 39 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8539 (tp) REVERT: I 239 MET cc_start: 0.3906 (tpt) cc_final: 0.3112 (tpt) REVERT: J 142 GLU cc_start: 0.8506 (tt0) cc_final: 0.8258 (tm-30) REVERT: J 799 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8610 (mmt-90) REVERT: J 1173 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5707 (mtp180) REVERT: K 70 GLN cc_start: 0.8288 (tt0) cc_final: 0.8059 (tm-30) REVERT: M 21 GLN cc_start: 0.4290 (OUTLIER) cc_final: 0.2500 (mm-40) outliers start: 70 outliers final: 17 residues processed: 374 average time/residue: 0.8826 time to fit residues: 390.2890 Evaluate side-chains 200 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 799 ARG Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 71 ASP Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 40.0000 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 516 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN G 294 ASN J 200 GLN J 430 HIS J1197 ASN K 15 ASN M 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.136629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077397 restraints weight = 110567.763| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.29 r_work: 0.2852 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43661 Z= 0.120 Angle : 0.496 11.730 59220 Z= 0.262 Chirality : 0.040 0.160 6708 Planarity : 0.004 0.055 7426 Dihedral : 12.013 67.193 6708 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 7.11 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 5199 helix: 1.65 (0.12), residues: 2092 sheet: 1.12 (0.22), residues: 574 loop : -0.37 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 296 TYR 0.014 0.001 TYR J 631 PHE 0.014 0.001 PHE A 324 TRP 0.007 0.001 TRP J 33 HIS 0.013 0.001 HIS M 284 Details of bonding type rmsd covalent geometry : bond 0.00270 (43653) covalent geometry : angle 0.49540 (59208) hydrogen bonds : bond 0.04077 ( 1825) hydrogen bonds : angle 4.47561 ( 5056) metal coordination : bond 0.00659 ( 8) metal coordination : angle 2.22680 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 190 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.1266 (mmm) cc_final: 0.0345 (ttt) REVERT: D 251 LEU cc_start: 0.1497 (OUTLIER) cc_final: 0.0886 (mt) REVERT: D 267 LYS cc_start: 0.5679 (pmtt) cc_final: 0.4441 (mmpt) REVERT: G 51 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.9225 (mmp) REVERT: G 228 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8446 (mp) REVERT: I 39 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8847 (tp) REVERT: I 239 MET cc_start: 0.3982 (tpt) cc_final: 0.3431 (tpt) REVERT: I 345 PRO cc_start: 0.8705 (Cg_endo) cc_final: 0.8337 (Cg_exo) REVERT: I 895 LEU cc_start: 0.9172 (mm) cc_final: 0.8944 (mm) REVERT: J 142 GLU cc_start: 0.9085 (tt0) cc_final: 0.8389 (tm-30) REVERT: J 218 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8277 (t) REVERT: K 72 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8033 (tm-30) REVERT: K 73 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8276 (mt0) REVERT: M 21 GLN cc_start: 0.3238 (OUTLIER) cc_final: 0.2073 (mm-40) outliers start: 72 outliers final: 26 residues processed: 240 average time/residue: 0.8088 time to fit residues: 236.9919 Evaluate side-chains 200 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 166 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 431 optimal weight: 0.8980 chunk 322 optimal weight: 5.9990 chunk 490 optimal weight: 0.0980 chunk 95 optimal weight: 30.0000 chunk 491 optimal weight: 1.9990 chunk 404 optimal weight: 0.5980 chunk 348 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN I 618 GLN J 430 HIS J1197 ASN K 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076838 restraints weight = 110375.259| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.86 r_work: 0.2867 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43661 Z= 0.092 Angle : 0.456 9.477 59220 Z= 0.240 Chirality : 0.039 0.246 6708 Planarity : 0.003 0.058 7426 Dihedral : 11.887 66.685 6686 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.29 % Allowed : 7.83 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5199 helix: 1.72 (0.12), residues: 2110 sheet: 1.22 (0.22), residues: 576 loop : -0.31 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 473 TYR 0.013 0.001 TYR M 303 PHE 0.014 0.001 PHE A 324 TRP 0.006 0.000 TRP J1020 HIS 0.004 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00203 (43653) covalent geometry : angle 0.45539 (59208) hydrogen bonds : bond 0.03496 ( 1825) hydrogen bonds : angle 4.18717 ( 5056) metal coordination : bond 0.00413 ( 8) metal coordination : angle 2.15436 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.1242 (mmm) cc_final: 0.0409 (ttt) REVERT: D 251 LEU cc_start: 0.1301 (OUTLIER) cc_final: 0.0811 (mt) REVERT: D 267 LYS cc_start: 0.5718 (pmtt) cc_final: 0.4825 (mmpt) REVERT: G 194 GLN cc_start: 0.8600 (pm20) cc_final: 0.8391 (pm20) REVERT: I 239 MET cc_start: 0.3357 (tpt) cc_final: 0.2968 (tpt) REVERT: I 545 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8052 (t80) REVERT: I 895 LEU cc_start: 0.9159 (mm) cc_final: 0.8946 (mm) REVERT: J 142 GLU cc_start: 0.8972 (tt0) cc_final: 0.8279 (tm-30) REVERT: J 795 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8488 (t80) REVERT: K 70 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6768 (tm-30) REVERT: M 21 GLN cc_start: 0.2273 (OUTLIER) cc_final: 0.1667 (mm-40) REVERT: M 365 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8554 (mtp) outliers start: 58 outliers final: 22 residues processed: 211 average time/residue: 0.7488 time to fit residues: 195.3232 Evaluate side-chains 190 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 220 optimal weight: 20.0000 chunk 42 optimal weight: 0.4980 chunk 235 optimal weight: 8.9990 chunk 476 optimal weight: 0.3980 chunk 74 optimal weight: 50.0000 chunk 491 optimal weight: 3.9990 chunk 457 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 390 optimal weight: 1.9990 chunk 406 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN J 430 HIS J1197 ASN K 15 ASN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076510 restraints weight = 110297.967| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.82 r_work: 0.2855 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 43661 Z= 0.093 Angle : 0.442 8.159 59220 Z= 0.232 Chirality : 0.039 0.180 6708 Planarity : 0.003 0.058 7426 Dihedral : 11.806 66.390 6675 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.38 % Allowed : 8.34 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5199 helix: 1.79 (0.12), residues: 2115 sheet: 1.30 (0.22), residues: 576 loop : -0.25 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 191 TYR 0.013 0.001 TYR J 631 PHE 0.012 0.001 PHE J1319 TRP 0.008 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00210 (43653) covalent geometry : angle 0.44058 (59208) hydrogen bonds : bond 0.03341 ( 1825) hydrogen bonds : angle 4.01097 ( 5056) metal coordination : bond 0.00411 ( 8) metal coordination : angle 2.09639 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.1208 (mmm) cc_final: 0.0541 (mtt) REVERT: D 251 LEU cc_start: 0.1289 (OUTLIER) cc_final: 0.0824 (mt) REVERT: D 267 LYS cc_start: 0.5627 (pmtt) cc_final: 0.4880 (mmpt) REVERT: I 239 MET cc_start: 0.3685 (tpt) cc_final: 0.3198 (tpt) REVERT: I 394 ARG cc_start: 0.9346 (mtt90) cc_final: 0.9129 (mtm-85) REVERT: I 545 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8335 (t80) REVERT: I 895 LEU cc_start: 0.9248 (mm) cc_final: 0.8992 (mm) REVERT: J 142 GLU cc_start: 0.9097 (tt0) cc_final: 0.8436 (tm-30) REVERT: J 795 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8629 (t80) REVERT: K 73 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8357 (mt0) REVERT: M 21 GLN cc_start: 0.3016 (OUTLIER) cc_final: 0.2009 (mm-40) REVERT: M 365 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8893 (mtp) outliers start: 62 outliers final: 23 residues processed: 219 average time/residue: 0.7590 time to fit residues: 205.2838 Evaluate side-chains 191 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 426 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 466 optimal weight: 2.9990 chunk 492 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 262 optimal weight: 0.0050 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN I 618 GLN J 430 HIS J1197 ASN K 15 ASN M 205 GLN M 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.135046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076170 restraints weight = 109475.760| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.19 r_work: 0.2812 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 43661 Z= 0.179 Angle : 0.492 8.501 59220 Z= 0.258 Chirality : 0.041 0.190 6708 Planarity : 0.004 0.057 7426 Dihedral : 11.882 66.814 6672 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 8.56 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 5199 helix: 1.75 (0.12), residues: 2113 sheet: 1.17 (0.22), residues: 594 loop : -0.30 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 974 TYR 0.017 0.001 TYR J 631 PHE 0.023 0.001 PHE J1037 TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00432 (43653) covalent geometry : angle 0.49063 (59208) hydrogen bonds : bond 0.04276 ( 1825) hydrogen bonds : angle 4.10071 ( 5056) metal coordination : bond 0.00810 ( 8) metal coordination : angle 2.35675 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.1208 (mmm) cc_final: 0.0542 (mtt) REVERT: D 380 LEU cc_start: -0.2584 (OUTLIER) cc_final: -0.2837 (mm) REVERT: I 165 HIS cc_start: 0.8767 (t-90) cc_final: 0.8443 (t70) REVERT: I 239 MET cc_start: 0.3997 (tpt) cc_final: 0.3386 (tpt) REVERT: I 545 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8374 (t80) REVERT: J 142 GLU cc_start: 0.9121 (tt0) cc_final: 0.8435 (tm-30) REVERT: J 330 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8917 (mmp) REVERT: J 795 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8568 (t80) REVERT: J 995 TYR cc_start: 0.7112 (m-80) cc_final: 0.6832 (m-80) REVERT: K 35 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7913 (mptm) REVERT: K 70 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7417 (tm-30) REVERT: M 21 GLN cc_start: 0.3509 (OUTLIER) cc_final: 0.2122 (mm-40) REVERT: M 306 MET cc_start: 0.8508 (mpp) cc_final: 0.8286 (mpt) REVERT: M 365 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8900 (mtp) outliers start: 65 outliers final: 31 residues processed: 212 average time/residue: 0.6334 time to fit residues: 166.5362 Evaluate side-chains 199 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 272 optimal weight: 0.7980 chunk 104 optimal weight: 50.0000 chunk 13 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 392 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 435 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN J 320 ASN J 430 HIS K 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074128 restraints weight = 109959.437| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.57 r_work: 0.2795 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 43661 Z= 0.200 Angle : 0.508 13.891 59220 Z= 0.267 Chirality : 0.041 0.198 6708 Planarity : 0.004 0.063 7426 Dihedral : 11.952 66.022 6672 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.47 % Allowed : 8.85 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 5199 helix: 1.66 (0.12), residues: 2120 sheet: 1.09 (0.22), residues: 598 loop : -0.33 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 191 TYR 0.017 0.001 TYR J 631 PHE 0.016 0.001 PHE J1319 TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00485 (43653) covalent geometry : angle 0.50730 (59208) hydrogen bonds : bond 0.04485 ( 1825) hydrogen bonds : angle 4.14118 ( 5056) metal coordination : bond 0.00910 ( 8) metal coordination : angle 2.46364 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 PHE cc_start: -0.1063 (m-80) cc_final: -0.1789 (m-80) REVERT: B 146 MET cc_start: 0.1261 (mmm) cc_final: 0.0525 (mtt) REVERT: D 380 LEU cc_start: -0.2744 (OUTLIER) cc_final: -0.2953 (mm) REVERT: I 205 PRO cc_start: 0.8322 (Cg_exo) cc_final: 0.8072 (Cg_endo) REVERT: I 239 MET cc_start: 0.3712 (tpt) cc_final: 0.2904 (tpt) REVERT: I 545 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8137 (t80) REVERT: I 895 LEU cc_start: 0.9168 (mm) cc_final: 0.8906 (mm) REVERT: I 1264 GLN cc_start: 0.8479 (mp10) cc_final: 0.8071 (mp10) REVERT: J 142 GLU cc_start: 0.8949 (tt0) cc_final: 0.8291 (tm-30) REVERT: J 795 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8446 (t80) REVERT: J 995 TYR cc_start: 0.6622 (m-80) cc_final: 0.6354 (m-80) REVERT: K 35 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7988 (mptm) REVERT: M 21 GLN cc_start: 0.3050 (OUTLIER) cc_final: 0.2094 (mm-40) REVERT: M 306 MET cc_start: 0.8443 (mpp) cc_final: 0.8230 (mpp) REVERT: M 365 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8779 (mtp) outliers start: 66 outliers final: 33 residues processed: 214 average time/residue: 0.6699 time to fit residues: 179.0696 Evaluate side-chains 201 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 247 optimal weight: 1.9990 chunk 426 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 385 optimal weight: 0.3980 chunk 258 optimal weight: 0.0670 chunk 326 optimal weight: 0.6980 chunk 460 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 328 optimal weight: 0.8980 chunk 491 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN J 430 HIS J1197 ASN K 15 ASN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.135878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075288 restraints weight = 107788.783| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.61 r_work: 0.2836 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 43661 Z= 0.089 Angle : 0.455 12.374 59220 Z= 0.239 Chirality : 0.039 0.147 6708 Planarity : 0.003 0.067 7426 Dihedral : 11.852 64.595 6672 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.05 % Allowed : 9.39 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 5199 helix: 1.85 (0.12), residues: 2121 sheet: 1.37 (0.23), residues: 554 loop : -0.24 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 191 TYR 0.012 0.001 TYR J 631 PHE 0.026 0.001 PHE J1037 TRP 0.008 0.001 TRP J 33 HIS 0.003 0.000 HIS I 832 Details of bonding type rmsd covalent geometry : bond 0.00195 (43653) covalent geometry : angle 0.45406 (59208) hydrogen bonds : bond 0.03267 ( 1825) hydrogen bonds : angle 3.91604 ( 5056) metal coordination : bond 0.00304 ( 8) metal coordination : angle 2.14276 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 PHE cc_start: 0.0474 (m-80) cc_final: -0.0412 (m-80) REVERT: B 146 MET cc_start: 0.1297 (mmm) cc_final: 0.0635 (mtt) REVERT: D 267 LYS cc_start: 0.5684 (pmtt) cc_final: 0.5004 (mmpt) REVERT: D 380 LEU cc_start: -0.2441 (OUTLIER) cc_final: -0.2669 (mm) REVERT: I 165 HIS cc_start: 0.8620 (t-90) cc_final: 0.8216 (t70) REVERT: I 239 MET cc_start: 0.3039 (tpt) cc_final: 0.2547 (tpt) REVERT: I 394 ARG cc_start: 0.9366 (mtt90) cc_final: 0.9075 (mtm-85) REVERT: I 545 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (t80) REVERT: I 895 LEU cc_start: 0.9186 (mm) cc_final: 0.8926 (mm) REVERT: J 142 GLU cc_start: 0.8906 (tt0) cc_final: 0.8242 (tm-30) REVERT: J 795 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8451 (t80) REVERT: J 992 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7653 (mppt) REVERT: J 995 TYR cc_start: 0.6224 (m-80) cc_final: 0.5927 (m-80) REVERT: J 1189 MET cc_start: 0.8442 (mpm) cc_final: 0.7596 (tpt) REVERT: K 73 GLN cc_start: 0.8207 (mt0) cc_final: 0.7989 (tm-30) REVERT: M 21 GLN cc_start: 0.2475 (OUTLIER) cc_final: 0.2067 (mm-40) REVERT: M 306 MET cc_start: 0.8449 (mpp) cc_final: 0.8201 (mpt) REVERT: M 365 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8764 (mtp) outliers start: 47 outliers final: 25 residues processed: 203 average time/residue: 0.4863 time to fit residues: 122.0325 Evaluate side-chains 196 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 992 LYS Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 48 optimal weight: 50.0000 chunk 322 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 342 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 454 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 449 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN J1197 ASN K 15 ASN K 62 GLN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076913 restraints weight = 110095.954| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.32 r_work: 0.2841 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 43661 Z= 0.113 Angle : 0.467 11.818 59220 Z= 0.243 Chirality : 0.039 0.146 6708 Planarity : 0.003 0.072 7426 Dihedral : 11.828 64.938 6672 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.94 % Allowed : 9.81 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.12), residues: 5199 helix: 1.86 (0.12), residues: 2125 sheet: 1.35 (0.23), residues: 552 loop : -0.24 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 191 TYR 0.015 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.009 0.001 TRP J1193 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00265 (43653) covalent geometry : angle 0.46601 (59208) hydrogen bonds : bond 0.03553 ( 1825) hydrogen bonds : angle 3.89743 ( 5056) metal coordination : bond 0.00518 ( 8) metal coordination : angle 2.11933 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 PHE cc_start: -0.0908 (m-80) cc_final: -0.1646 (m-80) REVERT: B 146 MET cc_start: 0.1247 (mmm) cc_final: 0.0505 (mtt) REVERT: D 267 LYS cc_start: 0.5436 (pmtt) cc_final: 0.4178 (mmpt) REVERT: I 165 HIS cc_start: 0.8716 (t-90) cc_final: 0.8461 (t70) REVERT: I 239 MET cc_start: 0.3998 (tpt) cc_final: 0.2996 (tpt) REVERT: I 394 ARG cc_start: 0.9323 (mtt90) cc_final: 0.9066 (mtm-85) REVERT: I 545 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8447 (t80) REVERT: I 1264 GLN cc_start: 0.8528 (mp10) cc_final: 0.8323 (mp10) REVERT: J 142 GLU cc_start: 0.9062 (tt0) cc_final: 0.8379 (tm-30) REVERT: J 795 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8575 (t80) REVERT: J 995 TYR cc_start: 0.7118 (m-80) cc_final: 0.6880 (m-80) REVERT: J 1189 MET cc_start: 0.8683 (mpm) cc_final: 0.7884 (tpt) REVERT: K 15 ASN cc_start: 0.7728 (t0) cc_final: 0.7427 (t0) REVERT: K 35 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7973 (mptm) REVERT: K 70 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7543 (tm-30) REVERT: M 21 GLN cc_start: 0.3889 (OUTLIER) cc_final: 0.2805 (mm-40) REVERT: M 365 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8994 (mtp) outliers start: 42 outliers final: 29 residues processed: 198 average time/residue: 0.4674 time to fit residues: 114.6775 Evaluate side-chains 196 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 236 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 347 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 chunk 338 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 453 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 323 HIS J 320 ASN J1197 ASN M 21 GLN ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.135096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074454 restraints weight = 109281.643| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.97 r_work: 0.2800 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 43661 Z= 0.140 Angle : 0.486 11.459 59220 Z= 0.253 Chirality : 0.040 0.154 6708 Planarity : 0.003 0.077 7426 Dihedral : 11.840 65.439 6672 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.85 % Allowed : 10.12 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5199 helix: 1.81 (0.12), residues: 2122 sheet: 1.26 (0.23), residues: 567 loop : -0.27 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 191 TYR 0.016 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.008 0.001 TRP J1193 HIS 0.012 0.001 HIS M 302 Details of bonding type rmsd covalent geometry : bond 0.00333 (43653) covalent geometry : angle 0.48503 (59208) hydrogen bonds : bond 0.03865 ( 1825) hydrogen bonds : angle 3.94457 ( 5056) metal coordination : bond 0.00644 ( 8) metal coordination : angle 2.22129 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 PHE cc_start: -0.0007 (m-80) cc_final: -0.0898 (m-80) REVERT: B 146 MET cc_start: 0.1258 (mmm) cc_final: 0.0582 (mtt) REVERT: I 205 PRO cc_start: 0.8316 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: I 239 MET cc_start: 0.3454 (tpt) cc_final: 0.2719 (tpt) REVERT: I 545 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8479 (t80) REVERT: I 895 LEU cc_start: 0.9213 (mm) cc_final: 0.8978 (mm) REVERT: I 996 ARG cc_start: 0.8931 (mmm160) cc_final: 0.8715 (mmm160) REVERT: J 1 MET cc_start: 0.6432 (tmt) cc_final: 0.6220 (tmt) REVERT: J 142 GLU cc_start: 0.9069 (tt0) cc_final: 0.8418 (tm-30) REVERT: J 795 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8552 (t80) REVERT: J 995 TYR cc_start: 0.6658 (m-80) cc_final: 0.6381 (m-80) REVERT: J 1189 MET cc_start: 0.8380 (mpm) cc_final: 0.7450 (tpt) REVERT: K 35 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8032 (mptm) REVERT: K 73 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8436 (mt0) REVERT: M 365 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8951 (mtp) outliers start: 38 outliers final: 27 residues processed: 192 average time/residue: 0.4465 time to fit residues: 106.6175 Evaluate side-chains 193 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 8 optimal weight: 50.0000 chunk 309 optimal weight: 0.8980 chunk 490 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 12 optimal weight: 50.0000 chunk 141 optimal weight: 8.9990 chunk 303 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1197 ASN K 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.134057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073481 restraints weight = 109789.224| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.59 r_work: 0.2772 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 43661 Z= 0.226 Angle : 0.547 11.792 59220 Z= 0.285 Chirality : 0.042 0.222 6708 Planarity : 0.004 0.084 7426 Dihedral : 11.940 65.512 6669 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 0.83 % Allowed : 10.24 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 5199 helix: 1.65 (0.12), residues: 2120 sheet: 1.08 (0.22), residues: 590 loop : -0.35 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 191 TYR 0.018 0.001 TYR J 631 PHE 0.018 0.001 PHE J1319 TRP 0.007 0.001 TRP J 236 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00550 (43653) covalent geometry : angle 0.54552 (59208) hydrogen bonds : bond 0.04778 ( 1825) hydrogen bonds : angle 4.13339 ( 5056) metal coordination : bond 0.01049 ( 8) metal coordination : angle 2.48584 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10398 Ramachandran restraints generated. 5199 Oldfield, 0 Emsley, 5199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 PHE cc_start: -0.1025 (m-80) cc_final: -0.1769 (m-80) REVERT: B 146 MET cc_start: 0.1232 (mmm) cc_final: 0.0504 (mtt) REVERT: I 205 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8157 (Cg_endo) REVERT: I 239 MET cc_start: 0.3766 (tpt) cc_final: 0.2917 (tpt) REVERT: I 545 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8183 (t80) REVERT: I 996 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8624 (mmm160) REVERT: I 1264 GLN cc_start: 0.8586 (mp10) cc_final: 0.8243 (mp10) REVERT: J 314 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8348 (mtt90) REVERT: J 795 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8406 (t80) REVERT: J 995 TYR cc_start: 0.6795 (m-80) cc_final: 0.6521 (m-80) REVERT: J 1189 MET cc_start: 0.8406 (mpm) cc_final: 0.7478 (tpt) REVERT: K 35 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7996 (mptm) REVERT: M 365 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8860 (mtp) outliers start: 37 outliers final: 26 residues processed: 188 average time/residue: 0.4577 time to fit residues: 106.2793 Evaluate side-chains 191 residues out of total 4493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 795 TYR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 11 optimal weight: 9.9990 chunk 356 optimal weight: 0.9980 chunk 494 optimal weight: 0.9990 chunk 69 optimal weight: 0.0070 chunk 467 optimal weight: 1.9990 chunk 50 optimal weight: 40.0000 chunk 66 optimal weight: 40.0000 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 320 ASN J1197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.135428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075596 restraints weight = 110327.204| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.71 r_work: 0.2831 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43661 Z= 0.103 Angle : 0.483 11.296 59220 Z= 0.252 Chirality : 0.039 0.145 6708 Planarity : 0.003 0.082 7426 Dihedral : 11.846 66.007 6669 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.71 % Allowed : 10.50 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 5199 helix: 1.79 (0.12), residues: 2132 sheet: 1.30 (0.23), residues: 560 loop : -0.28 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 191 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE J1319 TRP 0.011 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00235 (43653) covalent geometry : angle 0.48200 (59208) hydrogen bonds : bond 0.03520 ( 1825) hydrogen bonds : angle 3.93282 ( 5056) metal coordination : bond 0.00408 ( 8) metal coordination : angle 2.17246 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22945.09 seconds wall clock time: 387 minutes 51.32 seconds (23271.32 seconds total)