Starting phenix.real_space_refine on Sat Feb 7 02:19:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999.map" model { file = "/net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o19_49999/02_2026/9o19_49999_neut.cif" } resolution = 2.0 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= 0.002 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 94 5.16 5 C 17514 2.51 5 N 4851 2.21 5 O 6819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.03s 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: 29299 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3831 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 490} Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3872 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3846 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 17, 'TRANS': 491} Chain: "D" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3473 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 436} Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "F" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "G" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2132 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 933 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "W" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1345 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "X" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 714 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'TRANS': 94} Chain: "Y" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 696 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} 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: 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: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "B" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Classifications: {'water': 209} Link IDs: {None: 208} Chain: "C" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Classifications: {'water': 290} Link IDs: {None: 289} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 230 Classifications: {'water': 230} Link IDs: {None: 229} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.81, per 1000 atoms: 0.23 Number of scatterers: 29299 At special positions: 0 Unit cell: (173.47, 237.38, 176.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 16 15.00 Mg 5 11.99 O 6819 8.00 N 4851 7.00 C 17514 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6644 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 24 sheets defined 51.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.672A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.678A pdb=" N ARG A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 4.440A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.794A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.687A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.897A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 4.527A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 4.609A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 removed outlier: 4.567A pdb=" N LYS A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.741A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.744A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.678A pdb=" N ASN B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 4.511A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.760A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 300 removed outlier: 4.066A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 removed outlier: 3.506A pdb=" N VAL B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.556A pdb=" N ALA B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.566A pdb=" N ALA B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.511A pdb=" N MET B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 491 removed outlier: 4.497A pdb=" N LYS B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 11 through 18 removed outlier: 3.849A pdb=" N GLY C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.726A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 4.303A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.840A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.551A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.557A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.797A pdb=" N ALA C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 393 through 405 removed outlier: 3.522A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.777A pdb=" N LEU C 414 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.738A pdb=" N PHE C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.710A pdb=" N ARG D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.682A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 268 through 272 removed outlier: 3.601A pdb=" N GLY D 271 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.605A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 355 through 382 removed outlier: 3.684A pdb=" N TYR D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 437 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.544A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 462 removed outlier: 3.605A pdb=" N ALA D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.634A pdb=" N THR E 88 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.547A pdb=" N CYS E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 172 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.611A pdb=" N ARG E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.780A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 327 through 333 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 374 Processing helix chain 'E' and resid 375 through 383 Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.557A pdb=" N THR E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.577A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 462 removed outlier: 3.625A pdb=" N ALA E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 135 through 141 Processing helix chain 'F' and resid 159 through 174 Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 219 through 238 removed outlier: 5.554A pdb=" N ALA F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.768A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 removed outlier: 3.529A pdb=" N GLY F 271 " --> pdb=" O SER F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.770A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.918A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 327 through 333 removed outlier: 3.702A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.631A pdb=" N TYR F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 387 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 437 Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 453 through 461 removed outlier: 3.611A pdb=" N ALA F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 40 removed outlier: 3.816A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 60 removed outlier: 3.764A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 108 removed outlier: 4.177A pdb=" N GLY G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 130 removed outlier: 3.531A pdb=" N ALA G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 149 through 162 Processing helix chain 'G' and resid 210 through 285 removed outlier: 4.224A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA G 285 " --> pdb=" O GLY G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 101 removed outlier: 4.313A pdb=" N ALA H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 125 removed outlier: 4.264A pdb=" N ARG H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 22 Proline residue: W 10 - end of helix Processing helix chain 'W' and resid 24 through 40 Processing helix chain 'W' and resid 41 through 48 Processing helix chain 'W' and resid 54 through 67 Processing helix chain 'W' and resid 68 through 70 No H-bonds generated for 'chain 'W' and resid 68 through 70' Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'W' and resid 89 through 105 removed outlier: 3.774A pdb=" N ALA W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 Processing helix chain 'W' and resid 164 through 178 removed outlier: 3.578A pdb=" N SER W 178 " --> pdb=" O GLU W 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 120 removed outlier: 3.621A pdb=" N GLU X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 136 removed outlier: 3.512A pdb=" N VAL X 129 " --> pdb=" O GLY X 125 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS X 134 " --> pdb=" O THR X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 140 removed outlier: 3.866A pdb=" N ILE X 140 " --> pdb=" O GLY X 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 137 through 140' Processing helix chain 'X' and resid 142 through 154 removed outlier: 3.615A pdb=" N GLU X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL X 149 " --> pdb=" O HIS X 145 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS X 151 " --> pdb=" O GLN X 147 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA X 153 " --> pdb=" O VAL X 149 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 131 removed outlier: 3.547A pdb=" N VAL Y 129 " --> pdb=" O GLY Y 125 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR Y 130 " --> pdb=" O ALA Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 138 Processing helix chain 'Y' and resid 139 through 153 removed outlier: 3.849A pdb=" N HIS Y 145 " --> pdb=" O ASP Y 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.543A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 92 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE A 32 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL F 47 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 59 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.099A pdb=" N ALA A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 108 through 109 current: chain 'A' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 222 through 227 current: chain 'A' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 323 through 332 current: chain 'A' and resid 375 through 376 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.487A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.568A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE B 32 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.110A pdb=" N ALA B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 108 through 109 current: chain 'B' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 222 through 227 current: chain 'B' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 323 through 332 current: chain 'B' and resid 375 through 376 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.462A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 36 removed outlier: 5.575A pdb=" N ILE C 32 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR C 43 " --> pdb=" O ILE C 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 39 through 44 current: chain 'C' and resid 61 through 67 removed outlier: 6.573A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 72 through 76 current: chain 'E' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 23 current: chain 'E' and resid 44 through 52 removed outlier: 5.596A pdb=" N VAL E 47 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE E 59 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 60 current: chain 'W' and resid 137 through 144 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 137 through 144 current: chain 'W' and resid 159 through 162 Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.133A pdb=" N ALA C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 108 through 109 current: chain 'C' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 222 through 227 current: chain 'C' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 323 through 332 current: chain 'C' and resid 375 through 376 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.361A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 81 through 84 removed outlier: 4.489A pdb=" N GLU D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.323A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLN D 213 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL D 150 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 301 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU D 152 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.308A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.634A pdb=" N GLU E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.561A pdb=" N VAL E 184 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN E 248 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR E 302 " --> pdb=" O ASN E 248 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL E 150 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL E 301 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU E 152 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL E 324 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY E 151 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.360A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 81 through 84 removed outlier: 4.306A pdb=" N GLU F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.218A pdb=" N MET F 93 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL F 180 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL F 150 " --> pdb=" O GLN F 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 130 through 131 removed outlier: 4.557A pdb=" N PHE F 144 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 133 through 137 removed outlier: 7.868A pdb=" N VAL G 134 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU G 115 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA G 136 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL G 117 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE G 169 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY G 77 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.425A pdb=" N LEU G 206 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASP H 45 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY H 68 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS H 6 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL H 79 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP H 8 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA H 81 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL H 10 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 32 through 35 removed outlier: 3.630A pdb=" N MET H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N HIS H 27 " --> pdb=" O PRO H 50 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6260 1.33 - 1.46: 6105 1.46 - 1.58: 15791 1.58 - 1.71: 17 1.71 - 1.84: 171 Bond restraints: 28344 Sorted by residual: bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C ARG C 366 " pdb=" N PRO C 367 " ideal model delta sigma weight residual 1.336 1.394 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" C5 ADP D 501 " pdb=" C6 ADP D 501 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C GLN H 73 " pdb=" N PRO H 74 " ideal model delta sigma weight residual 1.337 1.377 -0.040 9.80e-03 1.04e+04 1.71e+01 ... (remaining 28339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 37744 4.43 - 8.85: 550 8.85 - 13.28: 41 13.28 - 17.70: 6 17.70 - 22.13: 1 Bond angle restraints: 38342 Sorted by residual: angle pdb=" C ASP E 247 " pdb=" N ASN E 248 " pdb=" CA ASN E 248 " ideal model delta sigma weight residual 123.13 108.41 14.72 1.51e+00 4.39e-01 9.50e+01 angle pdb=" CA PHE C 407 " pdb=" CB PHE C 407 " pdb=" CG PHE C 407 " ideal model delta sigma weight residual 113.80 121.64 -7.84 1.00e+00 1.00e+00 6.15e+01 angle pdb=" CA GLU X 146 " pdb=" CB GLU X 146 " pdb=" CG GLU X 146 " ideal model delta sigma weight residual 114.10 128.60 -14.50 2.00e+00 2.50e-01 5.26e+01 angle pdb=" CA LEU X 148 " pdb=" CB LEU X 148 " pdb=" CG LEU X 148 " ideal model delta sigma weight residual 116.30 138.43 -22.13 3.50e+00 8.16e-02 4.00e+01 angle pdb=" C LEU X 148 " pdb=" N VAL X 149 " pdb=" CA VAL X 149 " ideal model delta sigma weight residual 122.97 116.89 6.08 9.80e-01 1.04e+00 3.85e+01 ... (remaining 38337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 16763 34.26 - 68.52: 490 68.52 - 102.78: 47 102.78 - 137.04: 2 137.04 - 171.29: 4 Dihedral angle restraints: 17306 sinusoidal: 6890 harmonic: 10416 Sorted by residual: dihedral pdb=" C ASN E 248 " pdb=" N ASN E 248 " pdb=" CA ASN E 248 " pdb=" CB ASN E 248 " ideal model delta harmonic sigma weight residual -122.60 -144.58 21.98 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" N ASN E 248 " pdb=" C ASN E 248 " pdb=" CA ASN E 248 " pdb=" CB ASN E 248 " ideal model delta harmonic sigma weight residual 122.80 141.96 -19.16 0 2.50e+00 1.60e-01 5.87e+01 dihedral pdb=" C ASP E 247 " pdb=" N ASP E 247 " pdb=" CA ASP E 247 " pdb=" CB ASP E 247 " ideal model delta harmonic sigma weight residual -122.60 -141.70 19.10 0 2.50e+00 1.60e-01 5.83e+01 ... (remaining 17303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4253 0.168 - 0.337: 135 0.337 - 0.505: 3 0.505 - 0.673: 0 0.673 - 0.842: 2 Chirality restraints: 4393 Sorted by residual: chirality pdb=" CA ASN E 248 " pdb=" N ASN E 248 " pdb=" C ASN E 248 " pdb=" CB ASN E 248 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP E 247 " pdb=" N ASP E 247 " pdb=" C ASP E 247 " pdb=" CB ASP E 247 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CB VAL E 270 " pdb=" CA VAL E 270 " pdb=" CG1 VAL E 270 " pdb=" CG2 VAL E 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 4390 not shown) Planarity restraints: 5010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 159 " -0.057 2.00e-02 2.50e+03 1.15e-01 1.33e+02 pdb=" C GLY E 159 " 0.199 2.00e-02 2.50e+03 pdb=" O GLY E 159 " -0.075 2.00e-02 2.50e+03 pdb=" N LYS E 160 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 302 " 0.096 2.00e-02 2.50e+03 6.50e-02 8.45e+01 pdb=" CG TYR E 302 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 302 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 302 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR E 302 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR E 302 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR E 302 " -0.030 2.00e-02 2.50e+03 pdb=" OH TYR E 302 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 401 " 0.076 2.00e-02 2.50e+03 4.03e-02 3.24e+01 pdb=" CG TYR B 401 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 401 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 401 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 401 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 401 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 401 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 401 " 0.058 2.00e-02 2.50e+03 ... (remaining 5007 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 8 2.02 - 2.74: 1521 2.74 - 3.46: 41232 3.46 - 4.18: 77377 4.18 - 4.90: 128949 Nonbonded interactions: 249087 Sorted by model distance: nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 602 " model vdw 1.296 2.170 nonbonded pdb="MG MG A 602 " pdb=" O HOH A 719 " model vdw 1.562 2.170 nonbonded pdb="MG MG E 502 " pdb=" O HOH E 679 " model vdw 1.773 2.170 nonbonded pdb=" OE2 GLU E 279 " pdb=" O HOH E 601 " model vdw 1.816 3.040 nonbonded pdb=" OD2 ASP F 123 " pdb=" O HOH F 601 " model vdw 1.956 3.040 ... (remaining 249082 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 7 through 512 or resid 601 through 602)) selection = (chain 'B' and resid 7 through 602) selection = (chain 'C' and resid 7 through 602) } ncs_group { reference = (chain 'D' and (resid 8 through 463 or resid 501)) selection = (chain 'E' and resid 8 through 501) selection = (chain 'F' and resid 8 through 501) } ncs_group { reference = (chain 'X' and resid 62 through 154) selection = chain 'Y' } 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 29.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 : 0.009 0.120 28344 Z= 0.504 Angle : 1.406 22.129 38342 Z= 0.829 Chirality : 0.073 0.842 4393 Planarity : 0.013 0.177 5010 Dihedral : 16.071 171.295 10662 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.65 % Allowed : 11.88 % Favored : 87.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.12), residues: 3642 helix: -2.71 (0.09), residues: 1620 sheet: 0.20 (0.22), residues: 539 loop : -0.92 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG B 253 TYR 0.121 0.006 TYR E 302 PHE 0.053 0.005 PHE D 317 TRP 0.034 0.003 TRP A 139 HIS 0.024 0.003 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00910 (28344) covalent geometry : angle 1.40607 (38342) hydrogen bonds : bond 0.18250 ( 1384) hydrogen bonds : angle 7.09149 ( 3978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 286 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8222 (mtm-85) REVERT: A 394 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7454 (mp) REVERT: A 459 ASP cc_start: 0.7695 (p0) cc_final: 0.7461 (p0) REVERT: C 458 GLN cc_start: 0.7688 (mt0) cc_final: 0.7318 (mt0) REVERT: C 464 LYS cc_start: 0.7553 (mttt) cc_final: 0.6809 (tptt) REVERT: D 371 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7531 (mmm-85) REVERT: D 391 ASP cc_start: 0.7371 (m-30) cc_final: 0.7159 (m-30) REVERT: F 280 MET cc_start: 0.9190 (tpp) cc_final: 0.8874 (tpp) REVERT: F 450 MET cc_start: 0.8454 (mmt) cc_final: 0.8223 (mmm) REVERT: G 127 ARG cc_start: 0.5392 (ttp80) cc_final: 0.5084 (ttp-110) REVERT: G 243 MET cc_start: 0.8948 (ttp) cc_final: 0.8736 (ttp) REVERT: H 116 SER cc_start: 0.5834 (OUTLIER) cc_final: 0.5334 (p) REVERT: W 139 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7194 (mtm180) REVERT: X 93 GLN cc_start: 0.7505 (tp-100) cc_final: 0.7201 (tm-30) REVERT: X 148 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4412 (tm) REVERT: Y 81 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7424 (ttmt) REVERT: Y 149 VAL cc_start: 0.7974 (m) cc_final: 0.7678 (p) outliers start: 19 outliers final: 6 residues processed: 298 average time/residue: 0.8045 time to fit residues: 273.3068 Evaluate side-chains 220 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain X residue 148 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS A 409 GLN A 458 GLN A 480 HIS C 426 GLN C 477 GLN D 348 GLN E 437 ASN F 175 HIS H 6 HIS X 78 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087215 restraints weight = 34133.606| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.13 r_work: 0.3128 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28344 Z= 0.220 Angle : 0.723 9.717 38342 Z= 0.384 Chirality : 0.049 0.355 4393 Planarity : 0.006 0.073 5010 Dihedral : 9.434 167.281 4123 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.86 % Allowed : 10.40 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.27 (0.13), residues: 3642 helix: 0.47 (0.12), residues: 1629 sheet: 0.28 (0.20), residues: 587 loop : -0.01 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 253 TYR 0.019 0.002 TYR H 115 PHE 0.015 0.002 PHE E 432 TRP 0.009 0.002 TRP B 139 HIS 0.007 0.002 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00482 (28344) covalent geometry : angle 0.72296 (38342) hydrogen bonds : bond 0.07677 ( 1384) hydrogen bonds : angle 5.06507 ( 3978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8323 (mtt90) cc_final: 0.8118 (mtt90) REVERT: B 2 GLN cc_start: 0.7599 (pm20) cc_final: 0.7254 (pm20) REVERT: B 85 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 423 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7443 (mm-30) REVERT: C 458 GLN cc_start: 0.7796 (mt0) cc_final: 0.7406 (mt0) REVERT: C 464 LYS cc_start: 0.7887 (mttt) cc_final: 0.7178 (tttt) REVERT: D 371 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6856 (mmm-85) REVERT: D 391 ASP cc_start: 0.6917 (m-30) cc_final: 0.6621 (m-30) REVERT: E 26 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: E 53 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8179 (t0) REVERT: F 93 MET cc_start: 0.9239 (mtm) cc_final: 0.9015 (mtm) REVERT: F 202 ASN cc_start: 0.8585 (m-40) cc_final: 0.8229 (t0) REVERT: F 280 MET cc_start: 0.9412 (tpp) cc_final: 0.9086 (tpp) REVERT: F 450 MET cc_start: 0.8213 (mmt) cc_final: 0.7880 (mmm) REVERT: G 127 ARG cc_start: 0.5179 (ttp80) cc_final: 0.4932 (ttp-110) REVERT: G 243 MET cc_start: 0.8587 (ttp) cc_final: 0.8243 (ttp) REVERT: W 41 ASP cc_start: 0.8468 (t70) cc_final: 0.8196 (t70) REVERT: W 45 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7588 (ptp-110) REVERT: Y 81 LYS cc_start: 0.7307 (ttpp) cc_final: 0.7062 (ttmt) REVERT: Y 120 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7421 (mt) REVERT: Y 149 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7310 (p) outliers start: 54 outliers final: 17 residues processed: 266 average time/residue: 0.7952 time to fit residues: 242.2829 Evaluate side-chains 234 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 165 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 353 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN C 477 GLN W 52 GLN X 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.128457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090476 restraints weight = 34612.569| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.11 r_work: 0.3195 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28344 Z= 0.119 Angle : 0.539 9.459 38342 Z= 0.282 Chirality : 0.043 0.171 4393 Planarity : 0.004 0.043 5010 Dihedral : 8.658 160.775 4114 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.48 % Allowed : 10.99 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.25 (0.14), residues: 3642 helix: 1.57 (0.13), residues: 1636 sheet: 0.39 (0.21), residues: 576 loop : 0.30 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 253 TYR 0.015 0.001 TYR D 252 PHE 0.010 0.001 PHE C 355 TRP 0.006 0.001 TRP W 28 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00235 (28344) covalent geometry : angle 0.53932 (38342) hydrogen bonds : bond 0.05447 ( 1384) hydrogen bonds : angle 4.59427 ( 3978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.097 Fit side-chains REVERT: B 2 GLN cc_start: 0.7566 (pm20) cc_final: 0.7314 (pm20) REVERT: B 85 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: B 402 ARG cc_start: 0.7711 (mmt180) cc_final: 0.7460 (mtt-85) REVERT: C 427 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7444 (ttm-80) REVERT: C 458 GLN cc_start: 0.7827 (mt0) cc_final: 0.7376 (mt0) REVERT: C 464 LYS cc_start: 0.7845 (mttt) cc_final: 0.7172 (tttt) REVERT: D 371 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6810 (mmm-85) REVERT: D 391 ASP cc_start: 0.6919 (m-30) cc_final: 0.6627 (m-30) REVERT: D 394 LEU cc_start: 0.7534 (tt) cc_final: 0.7036 (tm) REVERT: E 26 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7715 (mtp180) REVERT: E 377 ASP cc_start: 0.7394 (p0) cc_final: 0.7133 (m-30) REVERT: F 93 MET cc_start: 0.9217 (mtm) cc_final: 0.8982 (mtm) REVERT: F 202 ASN cc_start: 0.8485 (m-40) cc_final: 0.8178 (t0) REVERT: F 280 MET cc_start: 0.9448 (tpp) cc_final: 0.9086 (tpp) REVERT: F 446 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7488 (mm-40) REVERT: F 450 MET cc_start: 0.8234 (mmt) cc_final: 0.7856 (mmm) REVERT: G 243 MET cc_start: 0.8620 (ttp) cc_final: 0.8389 (ttp) REVERT: W 45 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7561 (ptp-110) REVERT: W 103 GLU cc_start: 0.8070 (tp30) cc_final: 0.7469 (tm-30) REVERT: X 89 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6577 (mp0) REVERT: Y 81 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6984 (ttmt) REVERT: Y 120 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7330 (mm) REVERT: Y 149 VAL cc_start: 0.7660 (m) cc_final: 0.7390 (p) outliers start: 43 outliers final: 18 residues processed: 249 average time/residue: 0.8344 time to fit residues: 236.3554 Evaluate side-chains 225 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 257 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 458 GLN C 477 GLN C 480 HIS Y 63 GLN Y 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.125412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086807 restraints weight = 34042.566| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.11 r_work: 0.3131 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28344 Z= 0.226 Angle : 0.701 10.332 38342 Z= 0.372 Chirality : 0.050 0.324 4393 Planarity : 0.006 0.075 5010 Dihedral : 9.307 169.570 4114 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.96 % Allowed : 10.99 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.34 (0.14), residues: 3642 helix: 1.69 (0.13), residues: 1632 sheet: 0.25 (0.20), residues: 572 loop : 0.37 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 69 TYR 0.020 0.002 TYR H 115 PHE 0.015 0.002 PHE E 432 TRP 0.008 0.002 TRP B 139 HIS 0.007 0.002 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00502 (28344) covalent geometry : angle 0.70078 (38342) hydrogen bonds : bond 0.07312 ( 1384) hydrogen bonds : angle 4.92526 ( 3978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 1.112 Fit side-chains REVERT: A 157 MET cc_start: 0.8610 (mmp) cc_final: 0.8263 (mmm) REVERT: A 394 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 2 GLN cc_start: 0.7568 (pm20) cc_final: 0.7296 (pm20) REVERT: B 85 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 94 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7785 (mtm110) REVERT: B 95 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8611 (pp) REVERT: C 427 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6883 (mtm-85) REVERT: C 458 GLN cc_start: 0.7802 (mt0) cc_final: 0.7412 (mt0) REVERT: C 464 LYS cc_start: 0.7966 (mttt) cc_final: 0.7250 (tttt) REVERT: D 371 ARG cc_start: 0.7301 (mmm160) cc_final: 0.7000 (mmm-85) REVERT: D 386 GLU cc_start: 0.6581 (tp30) cc_final: 0.5856 (mp0) REVERT: D 391 ASP cc_start: 0.6980 (m-30) cc_final: 0.6699 (m-30) REVERT: F 93 MET cc_start: 0.9252 (mtm) cc_final: 0.9023 (mtm) REVERT: F 280 MET cc_start: 0.9404 (tpp) cc_final: 0.9089 (tpp) REVERT: F 328 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7487 (mtt90) REVERT: F 450 MET cc_start: 0.8204 (mmt) cc_final: 0.7851 (mmm) REVERT: G 243 MET cc_start: 0.8691 (ttp) cc_final: 0.8450 (ttp) REVERT: H 35 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.6039 (pp) REVERT: W 45 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7597 (ptp-170) REVERT: W 103 GLU cc_start: 0.8194 (tp30) cc_final: 0.7712 (tm-30) REVERT: Y 120 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7428 (mt) REVERT: Y 149 VAL cc_start: 0.7668 (m) cc_final: 0.7440 (p) outliers start: 57 outliers final: 29 residues processed: 253 average time/residue: 0.7605 time to fit residues: 220.8902 Evaluate side-chains 243 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 126 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 189 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 290 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 344 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 477 GLN Y 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090346 restraints weight = 34359.872| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.24 r_work: 0.3159 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28344 Z= 0.119 Angle : 0.534 8.171 38342 Z= 0.280 Chirality : 0.043 0.175 4393 Planarity : 0.003 0.038 5010 Dihedral : 8.672 162.468 4114 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.55 % Allowed : 11.51 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.75 (0.14), residues: 3642 helix: 2.13 (0.13), residues: 1643 sheet: 0.35 (0.20), residues: 588 loop : 0.48 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 253 TYR 0.016 0.001 TYR D 252 PHE 0.011 0.001 PHE A 410 TRP 0.005 0.001 TRP W 28 HIS 0.003 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00237 (28344) covalent geometry : angle 0.53447 (38342) hydrogen bonds : bond 0.05367 ( 1384) hydrogen bonds : angle 4.54384 ( 3978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 1.016 Fit side-chains REVERT: A 157 MET cc_start: 0.8491 (mmp) cc_final: 0.8175 (mmm) REVERT: A 394 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 2 GLN cc_start: 0.7573 (pm20) cc_final: 0.7253 (pm20) REVERT: B 85 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: B 94 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7648 (mtm110) REVERT: B 95 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 402 ARG cc_start: 0.7785 (mmt180) cc_final: 0.7502 (mtt-85) REVERT: C 427 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7388 (ttm-80) REVERT: C 458 GLN cc_start: 0.7786 (mt0) cc_final: 0.7353 (mt0) REVERT: C 464 LYS cc_start: 0.7923 (mttt) cc_final: 0.7190 (tttt) REVERT: D 371 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6775 (mmm-85) REVERT: D 391 ASP cc_start: 0.6870 (m-30) cc_final: 0.6579 (m-30) REVERT: D 394 LEU cc_start: 0.7480 (tt) cc_final: 0.7020 (tm) REVERT: E 26 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7677 (mtp180) REVERT: E 377 ASP cc_start: 0.7390 (p0) cc_final: 0.7128 (m-30) REVERT: F 280 MET cc_start: 0.9445 (tpp) cc_final: 0.9041 (tpp) REVERT: F 446 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7486 (mm-40) REVERT: F 450 MET cc_start: 0.8257 (mmt) cc_final: 0.7886 (mmm) REVERT: G 243 MET cc_start: 0.8576 (ttp) cc_final: 0.8359 (ttp) REVERT: H 35 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6050 (pp) REVERT: W 45 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7883 (ptp-170) REVERT: W 103 GLU cc_start: 0.8102 (tp30) cc_final: 0.7452 (tm-30) REVERT: X 89 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6403 (mt-10) REVERT: Y 108 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: Y 149 VAL cc_start: 0.7563 (m) cc_final: 0.7347 (p) outliers start: 45 outliers final: 14 residues processed: 243 average time/residue: 0.8044 time to fit residues: 223.4286 Evaluate side-chains 224 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain Y residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 66 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 299 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN X 143 ASN Y 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088132 restraints weight = 33964.640| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.23 r_work: 0.3118 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28344 Z= 0.180 Angle : 0.633 8.731 38342 Z= 0.334 Chirality : 0.047 0.271 4393 Planarity : 0.005 0.059 5010 Dihedral : 9.006 165.739 4114 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.79 % Allowed : 11.30 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.66 (0.14), residues: 3642 helix: 2.04 (0.13), residues: 1644 sheet: 0.29 (0.20), residues: 576 loop : 0.47 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 253 TYR 0.019 0.002 TYR H 115 PHE 0.014 0.002 PHE C 355 TRP 0.006 0.001 TRP B 139 HIS 0.006 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00392 (28344) covalent geometry : angle 0.63350 (38342) hydrogen bonds : bond 0.06588 ( 1384) hydrogen bonds : angle 4.75128 ( 3978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.053 Fit side-chains REVERT: A 157 MET cc_start: 0.8570 (mmp) cc_final: 0.8216 (mmm) REVERT: A 394 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 2 GLN cc_start: 0.7580 (pm20) cc_final: 0.7258 (pm20) REVERT: B 85 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: B 94 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7771 (mtm110) REVERT: B 95 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8573 (pp) REVERT: C 366 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6669 (mmt90) REVERT: C 427 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6770 (mtm-85) REVERT: C 458 GLN cc_start: 0.7774 (mt0) cc_final: 0.7326 (mt0) REVERT: C 464 LYS cc_start: 0.7972 (mttt) cc_final: 0.7229 (tttt) REVERT: D 371 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6811 (mmm-85) REVERT: D 391 ASP cc_start: 0.6881 (m-30) cc_final: 0.6643 (m-30) REVERT: D 394 LEU cc_start: 0.7458 (tt) cc_final: 0.6955 (tm) REVERT: D 427 ASP cc_start: 0.7425 (m-30) cc_final: 0.7083 (m-30) REVERT: E 26 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: F 280 MET cc_start: 0.9413 (tpp) cc_final: 0.9109 (tpp) REVERT: F 374 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: F 450 MET cc_start: 0.8223 (mmt) cc_final: 0.7869 (mmm) REVERT: G 243 MET cc_start: 0.8601 (ttp) cc_final: 0.8295 (ttp) REVERT: H 121 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.5085 (mtm180) REVERT: W 45 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: W 103 GLU cc_start: 0.8177 (tp30) cc_final: 0.7575 (tm-30) REVERT: W 174 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: Y 149 VAL cc_start: 0.7575 (m) cc_final: 0.7369 (p) outliers start: 52 outliers final: 28 residues processed: 246 average time/residue: 0.8199 time to fit residues: 229.5910 Evaluate side-chains 240 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain W residue 174 GLU Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 50 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 319 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN C 512 GLN F 358 HIS W 122 GLN Y 78 GLN Y 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087209 restraints weight = 34019.252| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.22 r_work: 0.3106 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28344 Z= 0.217 Angle : 0.688 10.279 38342 Z= 0.364 Chirality : 0.049 0.320 4393 Planarity : 0.005 0.071 5010 Dihedral : 9.048 169.695 4114 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 11.44 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.50 (0.14), residues: 3642 helix: 1.89 (0.13), residues: 1640 sheet: 0.20 (0.20), residues: 572 loop : 0.43 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 69 TYR 0.024 0.002 TYR H 115 PHE 0.015 0.002 PHE E 432 TRP 0.007 0.002 TRP B 139 HIS 0.008 0.002 HIS H 27 Details of bonding type rmsd covalent geometry : bond 0.00483 (28344) covalent geometry : angle 0.68760 (38342) hydrogen bonds : bond 0.07152 ( 1384) hydrogen bonds : angle 4.89234 ( 3978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 1.130 Fit side-chains REVERT: A 157 MET cc_start: 0.8568 (mmp) cc_final: 0.8227 (mmm) REVERT: A 394 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 2 GLN cc_start: 0.7545 (pm20) cc_final: 0.7224 (pm20) REVERT: B 85 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: B 94 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7804 (mtm110) REVERT: B 95 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8596 (pp) REVERT: C 366 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6468 (mmt90) REVERT: C 427 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6801 (mtm-85) REVERT: C 458 GLN cc_start: 0.7731 (mt0) cc_final: 0.7320 (mt0) REVERT: C 464 LYS cc_start: 0.8022 (mttt) cc_final: 0.7260 (tttt) REVERT: D 371 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6859 (mmm-85) REVERT: D 391 ASP cc_start: 0.6877 (m-30) cc_final: 0.6595 (m-30) REVERT: D 427 ASP cc_start: 0.7404 (m-30) cc_final: 0.7057 (m-30) REVERT: E 26 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7827 (mtp180) REVERT: F 280 MET cc_start: 0.9405 (tpp) cc_final: 0.9052 (tpp) REVERT: F 328 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7493 (mtt90) REVERT: F 450 MET cc_start: 0.8237 (mmt) cc_final: 0.7880 (mmm) REVERT: F 459 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7085 (mm-30) REVERT: G 243 MET cc_start: 0.8619 (ttp) cc_final: 0.8340 (ttp) REVERT: H 121 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.5081 (mtm180) REVERT: W 45 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (ptp-170) outliers start: 54 outliers final: 27 residues processed: 248 average time/residue: 0.8121 time to fit residues: 229.8795 Evaluate side-chains 241 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 223 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN Y 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088306 restraints weight = 34183.899| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.22 r_work: 0.3126 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28344 Z= 0.159 Angle : 0.603 8.260 38342 Z= 0.318 Chirality : 0.046 0.239 4393 Planarity : 0.004 0.050 5010 Dihedral : 8.800 165.997 4114 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.58 % Allowed : 11.75 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.69 (0.14), residues: 3642 helix: 2.08 (0.13), residues: 1647 sheet: 0.25 (0.20), residues: 575 loop : 0.47 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 253 TYR 0.020 0.002 TYR H 115 PHE 0.014 0.002 PHE C 355 TRP 0.005 0.001 TRP B 139 HIS 0.005 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00338 (28344) covalent geometry : angle 0.60325 (38342) hydrogen bonds : bond 0.06230 ( 1384) hydrogen bonds : angle 4.70969 ( 3978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 1.061 Fit side-chains REVERT: A 157 MET cc_start: 0.8526 (mmp) cc_final: 0.8198 (mmm) REVERT: A 394 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8128 (mp) REVERT: B 2 GLN cc_start: 0.7555 (pm20) cc_final: 0.7215 (pm20) REVERT: B 85 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: B 94 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7705 (mtm110) REVERT: B 95 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8584 (pp) REVERT: C 366 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6790 (mmt90) REVERT: C 427 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6745 (mtm-85) REVERT: C 458 GLN cc_start: 0.7770 (mt0) cc_final: 0.7356 (mt0) REVERT: C 464 LYS cc_start: 0.8001 (mttt) cc_final: 0.7223 (tttt) REVERT: D 86 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7785 (pttm) REVERT: D 371 ARG cc_start: 0.7195 (mmm160) cc_final: 0.6933 (mmm-85) REVERT: D 391 ASP cc_start: 0.6833 (m-30) cc_final: 0.6537 (m-30) REVERT: D 394 LEU cc_start: 0.7529 (tt) cc_final: 0.7051 (tm) REVERT: D 427 ASP cc_start: 0.7363 (m-30) cc_final: 0.7034 (m-30) REVERT: E 26 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7805 (mtp180) REVERT: F 280 MET cc_start: 0.9431 (tpp) cc_final: 0.9140 (tpp) REVERT: F 328 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7462 (mtt90) REVERT: F 450 MET cc_start: 0.8253 (mmt) cc_final: 0.7894 (mmm) REVERT: F 459 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7017 (mm-30) REVERT: G 243 MET cc_start: 0.8604 (ttp) cc_final: 0.8309 (ttp) REVERT: H 121 ARG cc_start: 0.5445 (OUTLIER) cc_final: 0.5203 (ttp-110) REVERT: W 45 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7909 (ptp-170) REVERT: W 103 GLU cc_start: 0.8129 (tp30) cc_final: 0.7591 (tm-30) outliers start: 46 outliers final: 28 residues processed: 241 average time/residue: 0.8445 time to fit residues: 232.0876 Evaluate side-chains 242 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 105 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 chunk 354 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 337 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN Y 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087479 restraints weight = 33927.266| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.23 r_work: 0.3104 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28344 Z= 0.210 Angle : 0.680 10.048 38342 Z= 0.360 Chirality : 0.049 0.313 4393 Planarity : 0.005 0.071 5010 Dihedral : 9.028 168.454 4114 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.79 % Allowed : 11.68 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.54 (0.14), residues: 3642 helix: 1.93 (0.13), residues: 1640 sheet: 0.20 (0.20), residues: 575 loop : 0.44 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 69 TYR 0.023 0.002 TYR H 115 PHE 0.015 0.002 PHE C 355 TRP 0.007 0.001 TRP B 139 HIS 0.006 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00466 (28344) covalent geometry : angle 0.67999 (38342) hydrogen bonds : bond 0.07046 ( 1384) hydrogen bonds : angle 4.86536 ( 3978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 1.142 Fit side-chains REVERT: A 157 MET cc_start: 0.8575 (mmp) cc_final: 0.8237 (mmm) REVERT: A 394 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 2 GLN cc_start: 0.7549 (pm20) cc_final: 0.7206 (pm20) REVERT: B 85 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 94 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7815 (mtm110) REVERT: B 95 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (pp) REVERT: C 366 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6497 (mmt90) REVERT: C 427 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6774 (mtm-85) REVERT: C 458 GLN cc_start: 0.7734 (mt0) cc_final: 0.7337 (mt0) REVERT: C 464 LYS cc_start: 0.8048 (mttt) cc_final: 0.7282 (tttt) REVERT: D 86 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: D 371 ARG cc_start: 0.7223 (mmm160) cc_final: 0.6951 (mmm-85) REVERT: D 391 ASP cc_start: 0.6798 (m-30) cc_final: 0.6509 (m-30) REVERT: D 394 LEU cc_start: 0.7484 (tt) cc_final: 0.7002 (tm) REVERT: D 427 ASP cc_start: 0.7377 (m-30) cc_final: 0.7028 (m-30) REVERT: F 280 MET cc_start: 0.9405 (tpp) cc_final: 0.9047 (tpp) REVERT: F 328 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7473 (mtt90) REVERT: F 450 MET cc_start: 0.8252 (mmt) cc_final: 0.7892 (mmm) REVERT: F 459 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7098 (mm-30) REVERT: G 243 MET cc_start: 0.8608 (ttp) cc_final: 0.8327 (ttp) REVERT: W 45 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7924 (ptp-170) outliers start: 52 outliers final: 29 residues processed: 244 average time/residue: 0.8151 time to fit residues: 227.1228 Evaluate side-chains 241 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 12 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 224 optimal weight: 0.2980 chunk 281 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN Y 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090160 restraints weight = 34090.352| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.26 r_work: 0.3156 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28344 Z= 0.120 Angle : 0.542 8.272 38342 Z= 0.283 Chirality : 0.043 0.176 4393 Planarity : 0.003 0.039 5010 Dihedral : 8.454 161.772 4114 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.34 % Allowed : 12.23 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.91 (0.14), residues: 3642 helix: 2.33 (0.13), residues: 1647 sheet: 0.30 (0.20), residues: 587 loop : 0.52 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 253 TYR 0.017 0.001 TYR H 115 PHE 0.014 0.001 PHE A 410 TRP 0.005 0.001 TRP W 28 HIS 0.003 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00239 (28344) covalent geometry : angle 0.54212 (38342) hydrogen bonds : bond 0.05259 ( 1384) hydrogen bonds : angle 4.51139 ( 3978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.060 Fit side-chains REVERT: A 16 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7902 (mtm-85) REVERT: A 157 MET cc_start: 0.8513 (mmp) cc_final: 0.8169 (mmm) REVERT: A 394 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 2 GLN cc_start: 0.7564 (pm20) cc_final: 0.7263 (pm20) REVERT: B 85 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: B 94 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7717 (mtm110) REVERT: B 95 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8558 (pp) REVERT: B 402 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7417 (mtt-85) REVERT: C 427 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7347 (ttm-80) REVERT: C 458 GLN cc_start: 0.7785 (mt0) cc_final: 0.7341 (mt0) REVERT: C 464 LYS cc_start: 0.7922 (mttt) cc_final: 0.7181 (tttt) REVERT: D 86 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7778 (pttm) REVERT: D 371 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6799 (mmm-85) REVERT: D 391 ASP cc_start: 0.6773 (m-30) cc_final: 0.6478 (m-30) REVERT: D 394 LEU cc_start: 0.7542 (tt) cc_final: 0.7098 (tm) REVERT: D 427 ASP cc_start: 0.7346 (m-30) cc_final: 0.7051 (m-30) REVERT: E 377 ASP cc_start: 0.7420 (p0) cc_final: 0.7149 (m-30) REVERT: F 280 MET cc_start: 0.9441 (tpp) cc_final: 0.9040 (tpp) REVERT: F 450 MET cc_start: 0.8285 (mmt) cc_final: 0.7915 (mmm) REVERT: F 459 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7019 (mm-30) REVERT: G 243 MET cc_start: 0.8571 (ttp) cc_final: 0.8342 (ttp) REVERT: H 121 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.6118 (ttp-110) REVERT: W 45 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7857 (ptp-170) REVERT: W 103 GLU cc_start: 0.8100 (tp30) cc_final: 0.7538 (tm-30) REVERT: Y 108 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7368 (mm-30) outliers start: 39 outliers final: 23 residues processed: 236 average time/residue: 0.7660 time to fit residues: 207.3566 Evaluate side-chains 234 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain W residue 45 ARG Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 333 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 477 GLN Y 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.126789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.089105 restraints weight = 34293.010| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.23 r_work: 0.3141 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28344 Z= 0.138 Angle : 0.573 8.479 38342 Z= 0.300 Chirality : 0.044 0.200 4393 Planarity : 0.004 0.040 5010 Dihedral : 8.560 162.404 4113 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.38 % Allowed : 12.30 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.90 (0.14), residues: 3642 helix: 2.32 (0.13), residues: 1646 sheet: 0.29 (0.20), residues: 587 loop : 0.53 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 253 TYR 0.018 0.001 TYR H 115 PHE 0.013 0.001 PHE C 355 TRP 0.005 0.001 TRP B 139 HIS 0.004 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00286 (28344) covalent geometry : angle 0.57294 (38342) hydrogen bonds : bond 0.05738 ( 1384) hydrogen bonds : angle 4.56628 ( 3978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22068.29 seconds wall clock time: 373 minutes 1.80 seconds (22381.80 seconds total)