Starting phenix.real_space_refine on Mon Apr 6 10:13:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.map" model { file = "/net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nsv_49753/04_2026/9nsv_49753.cif" } resolution = 2.19 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= -0.000 sd= 0.058 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 Mo 2 10.26 5 Fe 32 7.16 5 S 146 5.16 5 C 10182 2.51 5 N 2704 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17487 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3790 Classifications: {'peptide': 475} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 453} Chain: "B" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4204 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 494} Chain: "C" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 458} Chain: "D" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4180 Classifications: {'peptide': 519} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 491} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 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: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 250 Classifications: {'water': 250} Link IDs: {None: 249} Chain: "B" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 451 Classifications: {'water': 451} Link IDs: {None: 450} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "D" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 440 Classifications: {'water': 440} Link IDs: {None: 439} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 106.600 44.239 38.188 1.00 36.63 S ATOM 1160 SG CYS A 154 101.214 26.181 50.267 1.00 17.33 S ATOM 4557 SG CYS B 94 97.866 29.059 53.281 1.00 17.69 S ATOM 454 SG CYS A 62 100.443 32.051 47.867 1.00 18.76 S ATOM 641 SG CYS A 88 95.344 27.718 47.947 1.00 16.04 S ATOM 641 SG CYS A 88 95.344 27.718 47.947 1.00 16.04 S ATOM 5011 SG CYS B 152 96.970 24.057 51.625 1.00 20.04 S ATOM 4376 SG CYS B 69 91.158 27.930 53.294 1.00 14.29 S ATOM 4557 SG CYS B 94 97.866 29.059 53.281 1.00 17.69 S ATOM 10116 SG CYS C 275 29.907 53.263 38.191 1.00 35.27 S ATOM 9187 SG CYS C 154 35.261 71.285 50.220 1.00 17.16 S ATOM 12560 SG CYS D 94 38.662 68.456 53.295 1.00 17.96 S ATOM 8481 SG CYS C 62 36.047 65.463 47.837 1.00 18.06 S ATOM 8668 SG CYS C 88 41.100 69.751 47.948 1.00 16.12 S ATOM 8668 SG CYS C 88 41.100 69.751 47.948 1.00 16.12 S ATOM 13014 SG CYS D 152 39.580 73.431 51.659 1.00 20.46 S ATOM 12379 SG CYS D 69 45.363 69.535 53.233 1.00 13.48 S ATOM 12560 SG CYS D 94 38.662 68.456 53.295 1.00 17.96 S Time building chain proxies: 4.33, per 1000 atoms: 0.25 Number of scatterers: 17487 At special positions: 0 Unit cell: (135.2, 98.15, 98.15, 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) Mo 2 41.97 Fe 32 26.01 S 146 16.00 O 4421 8.00 N 2704 7.00 C 10182 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 724.5 milliseconds 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 58.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.309A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 4.152A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.564A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.278A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.472A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.861A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.508A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.154A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.527A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.455A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.418A pdb=" N TYR A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.616A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 4.222A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.652A pdb=" N ARG B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.938A pdb=" N GLY B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 removed outlier: 4.060A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 126 through 142 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 191 through 209 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.758A pdb=" N PHE B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 293 through 296 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 321 through 336 Processing helix chain 'B' and resid 340 through 362 removed outlier: 5.166A pdb=" N THR B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TRP B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.605A pdb=" N ALA B 416 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 446 through 458 removed outlier: 4.129A pdb=" N ILE B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 462 Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 484 through 508 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.068A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.140A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.538A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.282A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.818A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.726A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 removed outlier: 4.112A pdb=" N LYS C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.367A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.427A pdb=" N TYR C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.572A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.979A pdb=" N LEU C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.943A pdb=" N GLY D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 removed outlier: 4.184A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 126 through 142 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 191 through 209 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.741A pdb=" N PHE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 293 through 296 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 321 through 336 Processing helix chain 'D' and resid 340 through 362 removed outlier: 5.214A pdb=" N THR D 359 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.636A pdb=" N SER D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 removed outlier: 3.600A pdb=" N ALA D 416 " --> pdb=" O PRO D 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 416' Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 446 through 458 removed outlier: 4.174A pdb=" N ILE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 462 Processing helix chain 'D' and resid 477 through 481 Processing helix chain 'D' and resid 484 through 508 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.726A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.097A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.996A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 114 removed outlier: 8.473A pdb=" N VAL B 113 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AA6, first strand: chain 'B' and resid 419 through 422 removed outlier: 8.315A pdb=" N GLU B 419 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 390 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS B 421 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 392 " --> pdb=" O HIS B 421 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE B 366 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU B 393 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 368 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS B 365 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 442 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 367 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N MET B 441 " --> pdb=" O ILE B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.673A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.088A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.397A pdb=" N VAL C 223 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AB2, first strand: chain 'D' and resid 250 through 252 Processing sheet with id=AB3, first strand: chain 'D' and resid 419 through 422 removed outlier: 8.323A pdb=" N GLU D 419 " --> pdb=" O GLU D 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 390 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N HIS D 421 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 392 " --> pdb=" O HIS D 421 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE D 366 " --> pdb=" O HIS D 391 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU D 393 " --> pdb=" O PHE D 366 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 368 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS D 365 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE D 442 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 367 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET D 441 " --> pdb=" O ILE D 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 780 hydrogen bonds defined for protein. 2256 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: 3.25 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 16217 1.57 - 1.92: 196 1.92 - 2.27: 46 2.27 - 2.61: 72 2.61 - 2.96: 18 Bond restraints: 16549 Sorted by residual: bond pdb="FE2 CLF D 702 " pdb="FE8 CLF D 702 " ideal model delta sigma weight residual 2.200 2.962 -0.762 2.00e-02 2.50e+03 1.45e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.958 -0.758 2.00e-02 2.50e+03 1.44e+03 bond pdb="FE4 CLF D 702 " pdb="FE5 CLF D 702 " ideal model delta sigma weight residual 2.200 2.906 -0.706 2.00e-02 2.50e+03 1.25e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.896 -0.696 2.00e-02 2.50e+03 1.21e+03 bond pdb="FE6 CLF B 601 " pdb="FE7 CLF B 601 " ideal model delta sigma weight residual 2.200 2.860 -0.660 2.00e-02 2.50e+03 1.09e+03 ... (remaining 16544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 22320 6.86 - 13.72: 3 13.72 - 20.58: 2 20.58 - 27.45: 0 27.45 - 34.31: 4 Bond angle restraints: 22329 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.69 34.31 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 702 " pdb="FE2 CLF D 702 " pdb="FE4 CLF D 702 " ideal model delta sigma weight residual 90.00 55.78 34.22 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF D 702 " pdb="FE2 CLF D 702 " pdb="FE1 CLF D 702 " ideal model delta sigma weight residual 90.00 57.07 32.93 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 57.08 32.92 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF D 702 " pdb="FE2 CLF D 702 " pdb="FE3 CLF D 702 " ideal model delta sigma weight residual 90.00 106.81 -16.81 3.00e+00 1.11e-01 3.14e+01 ... (remaining 22324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8919 17.89 - 35.79: 871 35.79 - 53.68: 253 53.68 - 71.57: 71 71.57 - 89.47: 41 Dihedral angle restraints: 10155 sinusoidal: 4413 harmonic: 5742 Sorted by residual: dihedral pdb=" CA ASP D 515 " pdb=" C ASP D 515 " pdb=" N TYR D 516 " pdb=" CA TYR D 516 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ASP B 515 " pdb=" C ASP B 515 " pdb=" N TYR B 516 " pdb=" CA TYR B 516 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ILE C 75 " pdb=" C ILE C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1324 0.029 - 0.058: 650 0.058 - 0.086: 207 0.086 - 0.115: 123 0.115 - 0.144: 22 Chirality restraints: 2326 Sorted by residual: chirality pdb=" CA ILE D 317 " pdb=" N ILE D 317 " pdb=" C ILE D 317 " pdb=" CB ILE D 317 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 317 " pdb=" N ILE B 317 " pdb=" C ILE B 317 " pdb=" CB ILE B 317 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE D 174 " pdb=" N ILE D 174 " pdb=" C ILE D 174 " pdb=" CB ILE D 174 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2323 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 360 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO C 74 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 74 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 18 2.62 - 3.19: 17061 3.19 - 3.76: 34436 3.76 - 4.33: 50507 4.33 - 4.90: 72712 Nonbonded interactions: 174734 Sorted by model distance: nonbonded pdb=" OD2 ASP D 356 " pdb="FE FE D 701 " model vdw 2.052 2.260 nonbonded pdb=" OD2 ASP B 356 " pdb="FE FE B 602 " model vdw 2.102 2.260 nonbonded pdb=" OE2 GLU B 108 " pdb="FE FE D 701 " model vdw 2.151 2.260 nonbonded pdb=" OD2 ASP D 352 " pdb="FE FE D 701 " model vdw 2.160 2.260 nonbonded pdb=" OD2 ASP B 352 " pdb="FE FE B 602 " model vdw 2.175 2.260 ... (remaining 174729 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' selection = (chain 'C' and resid 6 through 502) } ncs_group { reference = (chain 'B' and resid 4 through 522) selection = (chain 'D' and resid 4 through 522) } 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: 13.700 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.024 0.762 16565 Z= 1.266 Angle : 0.706 34.307 22329 Z= 0.321 Chirality : 0.042 0.144 2326 Planarity : 0.004 0.053 2884 Dihedral : 16.945 89.468 6485 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.67 % Allowed : 12.94 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.38 (0.18), residues: 1988 helix: 1.01 (0.16), residues: 962 sheet: -0.57 (0.36), residues: 206 loop : -0.31 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 97 TYR 0.021 0.002 TYR A 229 PHE 0.011 0.001 PHE B 43 TRP 0.022 0.002 TRP C 253 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.02337 (16549) covalent geometry : angle 0.70600 (22329) hydrogen bonds : bond 0.18123 ( 780) hydrogen bonds : angle 7.62777 ( 2256) Misc. bond : bond 0.16126 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.522 Fit side-chains REVERT: A 26 LYS cc_start: 0.7387 (mttt) cc_final: 0.6646 (mmtm) REVERT: A 168 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8275 (ttpp) REVERT: A 172 LYS cc_start: 0.8471 (tmtp) cc_final: 0.7722 (tmmt) REVERT: A 208 SER cc_start: 0.8449 (p) cc_final: 0.8196 (p) REVERT: A 217 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6908 (tm-30) REVERT: A 318 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7419 (tm-30) REVERT: A 347 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 415 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6994 (tptp) REVERT: A 445 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: A 473 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8068 (mttp) REVERT: A 476 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 142 LYS cc_start: 0.8647 (mptt) cc_final: 0.8138 (mmpt) REVERT: C 1 MET cc_start: 0.1625 (tpp) cc_final: 0.0661 (ttm) REVERT: C 26 LYS cc_start: 0.7689 (mttt) cc_final: 0.6939 (mmtm) REVERT: C 172 LYS cc_start: 0.8215 (tttt) cc_final: 0.7798 (tmmt) REVERT: C 217 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7304 (tm-30) REVERT: C 322 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7614 (ttpt) REVERT: C 345 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7282 (mtp180) REVERT: C 415 LYS cc_start: 0.7363 (tptp) cc_final: 0.7038 (tptp) REVERT: C 445 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: C 473 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8096 (mptt) REVERT: C 476 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: D 142 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8129 (mmpt) outliers start: 29 outliers final: 16 residues processed: 226 average time/residue: 0.7774 time to fit residues: 192.0660 Evaluate side-chains 234 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 142 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN D 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112189 restraints weight = 13105.607| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.83 r_work: 0.3188 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 16565 Z= 0.196 Angle : 0.729 29.166 22329 Z= 0.347 Chirality : 0.045 0.147 2326 Planarity : 0.004 0.066 2884 Dihedral : 6.907 75.152 2563 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 12.82 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.54 (0.19), residues: 1988 helix: 1.15 (0.16), residues: 998 sheet: -0.58 (0.36), residues: 194 loop : -0.29 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.020 0.002 TYR A 229 PHE 0.012 0.002 PHE C 431 TRP 0.018 0.002 TRP C 253 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00403 (16549) covalent geometry : angle 0.72872 (22329) hydrogen bonds : bond 0.05529 ( 780) hydrogen bonds : angle 5.95600 ( 2256) Misc. bond : bond 0.10338 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.726 Fit side-chains REVERT: A 26 LYS cc_start: 0.7408 (mttt) cc_final: 0.6668 (mmtm) REVERT: A 172 LYS cc_start: 0.8477 (tmtp) cc_final: 0.7786 (tmmt) REVERT: A 176 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: A 217 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6917 (tm-30) REVERT: A 318 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7322 (tm-30) REVERT: A 415 LYS cc_start: 0.7585 (tppt) cc_final: 0.6963 (tptp) REVERT: A 445 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: A 473 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7994 (mptt) REVERT: A 476 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: B 142 LYS cc_start: 0.8647 (mptt) cc_final: 0.8103 (mmpt) REVERT: C 26 LYS cc_start: 0.7526 (mttt) cc_final: 0.6799 (mmtm) REVERT: C 172 LYS cc_start: 0.8166 (tttt) cc_final: 0.7768 (tmmt) REVERT: C 217 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7303 (tm-30) REVERT: C 345 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7267 (mtp180) REVERT: C 415 LYS cc_start: 0.7443 (tptp) cc_final: 0.6979 (tptp) REVERT: C 445 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: C 473 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7903 (mptt) REVERT: D 142 LYS cc_start: 0.8689 (mttp) cc_final: 0.8110 (mmpt) REVERT: D 400 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7905 (mtp-110) outliers start: 33 outliers final: 12 residues processed: 233 average time/residue: 0.7456 time to fit residues: 190.6683 Evaluate side-chains 222 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 35 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114998 restraints weight = 13186.729| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.83 r_work: 0.3228 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 16565 Z= 0.150 Angle : 0.688 29.128 22329 Z= 0.321 Chirality : 0.043 0.143 2326 Planarity : 0.004 0.051 2884 Dihedral : 6.020 69.063 2528 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 12.88 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.66 (0.19), residues: 1988 helix: 1.31 (0.16), residues: 996 sheet: -0.59 (0.36), residues: 199 loop : -0.31 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.018 0.002 TYR A 229 PHE 0.010 0.001 PHE C 409 TRP 0.021 0.002 TRP C 253 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00301 (16549) covalent geometry : angle 0.68761 (22329) hydrogen bonds : bond 0.04570 ( 780) hydrogen bonds : angle 5.66277 ( 2256) Misc. bond : bond 0.08365 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.678 Fit side-chains REVERT: A 26 LYS cc_start: 0.7354 (mttt) cc_final: 0.6627 (mmtm) REVERT: A 168 LYS cc_start: 0.8598 (mttt) cc_final: 0.8180 (ttpp) REVERT: A 172 LYS cc_start: 0.8436 (tmtp) cc_final: 0.7743 (tmmt) REVERT: A 176 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (mtpp) REVERT: A 208 SER cc_start: 0.8416 (p) cc_final: 0.8171 (p) REVERT: A 217 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6928 (tm-30) REVERT: A 318 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7325 (tm-30) REVERT: A 322 LYS cc_start: 0.8182 (tttt) cc_final: 0.7598 (ttpp) REVERT: A 347 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 415 LYS cc_start: 0.7654 (tppt) cc_final: 0.7010 (tptp) REVERT: A 445 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: A 473 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7953 (mptt) REVERT: A 476 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: B 142 LYS cc_start: 0.8595 (mptt) cc_final: 0.8087 (mmpt) REVERT: C 1 MET cc_start: 0.1737 (tpp) cc_final: 0.0717 (ttm) REVERT: C 26 LYS cc_start: 0.7539 (mttt) cc_final: 0.6835 (mmtm) REVERT: C 172 LYS cc_start: 0.8127 (tttt) cc_final: 0.7740 (tmmt) REVERT: C 176 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8063 (mttp) REVERT: C 217 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7294 (tm-30) REVERT: C 345 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7283 (mtp180) REVERT: C 347 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: C 415 LYS cc_start: 0.7518 (tptp) cc_final: 0.7016 (tptp) REVERT: C 445 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: C 473 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7883 (mptt) REVERT: D 142 LYS cc_start: 0.8703 (mttp) cc_final: 0.8141 (mmpt) REVERT: D 237 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8629 (mtt180) REVERT: D 400 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7888 (mtp-110) outliers start: 34 outliers final: 16 residues processed: 246 average time/residue: 0.7702 time to fit residues: 207.7784 Evaluate side-chains 230 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN D 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110542 restraints weight = 13053.100| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 0.82 r_work: 0.3171 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 16565 Z= 0.238 Angle : 0.759 29.368 22329 Z= 0.365 Chirality : 0.048 0.152 2326 Planarity : 0.005 0.078 2884 Dihedral : 6.398 70.225 2525 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.47 % Allowed : 12.42 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.57 (0.18), residues: 1988 helix: 1.18 (0.16), residues: 1000 sheet: -0.53 (0.37), residues: 194 loop : -0.32 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.021 0.003 TYR A 229 PHE 0.015 0.002 PHE C 431 TRP 0.016 0.002 TRP C 253 HIS 0.005 0.001 HIS D 479 Details of bonding type rmsd covalent geometry : bond 0.00504 (16549) covalent geometry : angle 0.75915 (22329) hydrogen bonds : bond 0.05513 ( 780) hydrogen bonds : angle 5.78462 ( 2256) Misc. bond : bond 0.10820 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.666 Fit side-chains REVERT: A 26 LYS cc_start: 0.7436 (mttt) cc_final: 0.6698 (mmtm) REVERT: A 168 LYS cc_start: 0.8592 (mttt) cc_final: 0.8196 (ttpp) REVERT: A 172 LYS cc_start: 0.8493 (tmtp) cc_final: 0.7787 (tmmt) REVERT: A 176 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7930 (mmtp) REVERT: A 217 GLU cc_start: 0.7826 (mm-30) cc_final: 0.6922 (tm-30) REVERT: A 318 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7375 (tm-30) REVERT: A 347 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: A 415 LYS cc_start: 0.7637 (tppt) cc_final: 0.6982 (tptp) REVERT: A 445 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: A 473 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8029 (mptt) REVERT: A 476 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 142 LYS cc_start: 0.8651 (mptt) cc_final: 0.8154 (mmpt) REVERT: C 26 LYS cc_start: 0.7568 (mttt) cc_final: 0.6839 (mmtm) REVERT: C 172 LYS cc_start: 0.8211 (tttt) cc_final: 0.7773 (tmmt) REVERT: C 217 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7317 (tm-30) REVERT: C 287 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: C 345 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7295 (mtp180) REVERT: C 415 LYS cc_start: 0.7522 (tptp) cc_final: 0.6976 (tptp) REVERT: C 445 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: C 473 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7950 (mptt) REVERT: C 476 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: D 142 LYS cc_start: 0.8704 (mttp) cc_final: 0.8170 (mmpt) REVERT: D 176 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7923 (t0) REVERT: D 237 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8866 (mtt180) REVERT: D 400 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7921 (mtp-110) outliers start: 43 outliers final: 20 residues processed: 232 average time/residue: 0.7663 time to fit residues: 195.1492 Evaluate side-chains 231 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 3 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 chunk 157 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112914 restraints weight = 13144.758| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.83 r_work: 0.3201 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 16565 Z= 0.175 Angle : 0.713 29.184 22329 Z= 0.336 Chirality : 0.045 0.145 2326 Planarity : 0.004 0.066 2884 Dihedral : 6.249 70.735 2525 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 12.71 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.62 (0.18), residues: 1988 helix: 1.26 (0.16), residues: 997 sheet: -0.54 (0.37), residues: 194 loop : -0.33 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.020 0.002 TYR A 229 PHE 0.012 0.002 PHE C 431 TRP 0.021 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (16549) covalent geometry : angle 0.71307 (22329) hydrogen bonds : bond 0.04777 ( 780) hydrogen bonds : angle 5.62982 ( 2256) Misc. bond : bond 0.09096 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.636 Fit side-chains REVERT: A 26 LYS cc_start: 0.7382 (mttt) cc_final: 0.6639 (mmtm) REVERT: A 168 LYS cc_start: 0.8579 (mttt) cc_final: 0.8193 (ttpp) REVERT: A 172 LYS cc_start: 0.8456 (tmtp) cc_final: 0.7756 (tmmt) REVERT: A 176 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7894 (mmtp) REVERT: A 217 GLU cc_start: 0.7797 (mm-30) cc_final: 0.6922 (tm-30) REVERT: A 318 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7342 (tm-30) REVERT: A 322 LYS cc_start: 0.8188 (tttt) cc_final: 0.7581 (ttpp) REVERT: A 347 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: A 415 LYS cc_start: 0.7592 (tppt) cc_final: 0.6941 (tptp) REVERT: A 445 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: A 473 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7964 (mptt) REVERT: A 476 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: B 142 LYS cc_start: 0.8618 (mptt) cc_final: 0.8118 (mmpt) REVERT: C 1 MET cc_start: 0.1711 (tpp) cc_final: 0.0652 (ttm) REVERT: C 4 MET cc_start: 0.6237 (mtt) cc_final: 0.5870 (ttm) REVERT: C 26 LYS cc_start: 0.7522 (mttt) cc_final: 0.6807 (mmtm) REVERT: C 172 LYS cc_start: 0.8168 (tttt) cc_final: 0.7729 (tmmt) REVERT: C 217 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7315 (tm-30) REVERT: C 287 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 345 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7264 (mtp180) REVERT: C 347 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: C 415 LYS cc_start: 0.7510 (tptp) cc_final: 0.6963 (tptp) REVERT: C 445 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: C 473 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7895 (mptt) REVERT: C 476 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: D 142 LYS cc_start: 0.8677 (mttp) cc_final: 0.8166 (mmpt) REVERT: D 176 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7931 (t0) REVERT: D 237 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8800 (mtt180) REVERT: D 400 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7888 (mtp-110) outliers start: 39 outliers final: 19 residues processed: 234 average time/residue: 0.7496 time to fit residues: 192.5846 Evaluate side-chains 235 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 192 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114869 restraints weight = 13061.283| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.82 r_work: 0.3224 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 16565 Z= 0.151 Angle : 0.693 29.136 22329 Z= 0.323 Chirality : 0.044 0.142 2326 Planarity : 0.004 0.058 2884 Dihedral : 6.109 70.270 2525 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.30 % Allowed : 12.94 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.69 (0.19), residues: 1988 helix: 1.35 (0.16), residues: 996 sheet: -0.57 (0.36), residues: 199 loop : -0.33 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.019 0.002 TYR A 229 PHE 0.010 0.001 PHE C 431 TRP 0.021 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00306 (16549) covalent geometry : angle 0.69280 (22329) hydrogen bonds : bond 0.04389 ( 780) hydrogen bonds : angle 5.52053 ( 2256) Misc. bond : bond 0.08115 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.631 Fit side-chains REVERT: A 7 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.5279 (t70) REVERT: A 11 SER cc_start: 0.6697 (m) cc_final: 0.6388 (p) REVERT: A 26 LYS cc_start: 0.7380 (mttt) cc_final: 0.6641 (mmtm) REVERT: A 168 LYS cc_start: 0.8549 (mttt) cc_final: 0.8170 (ttpp) REVERT: A 172 LYS cc_start: 0.8425 (tmtp) cc_final: 0.7711 (tmmt) REVERT: A 217 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6919 (tm-30) REVERT: A 318 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7298 (tm-30) REVERT: A 347 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: A 415 LYS cc_start: 0.7584 (tppt) cc_final: 0.6935 (tptp) REVERT: A 445 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: A 473 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7938 (mptt) REVERT: A 476 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: B 120 ASP cc_start: 0.7474 (m-30) cc_final: 0.7272 (m-30) REVERT: B 142 LYS cc_start: 0.8578 (mptt) cc_final: 0.8086 (mmpt) REVERT: C 1 MET cc_start: 0.1793 (tpp) cc_final: 0.0781 (ttm) REVERT: C 26 LYS cc_start: 0.7511 (mttt) cc_final: 0.6793 (mmtm) REVERT: C 172 LYS cc_start: 0.8161 (tttt) cc_final: 0.7732 (tmmt) REVERT: C 176 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7962 (mtpp) REVERT: C 217 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7298 (tm-30) REVERT: C 287 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: C 345 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7258 (mtp180) REVERT: C 347 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: C 392 LYS cc_start: 0.7237 (mptp) cc_final: 0.6147 (pmtt) REVERT: C 415 LYS cc_start: 0.7512 (tptp) cc_final: 0.6937 (tptp) REVERT: C 445 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: C 473 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7888 (mptt) REVERT: C 476 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: D 142 LYS cc_start: 0.8658 (mttp) cc_final: 0.8171 (mmpt) REVERT: D 237 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8630 (mtt180) REVERT: D 400 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7888 (mtp-110) outliers start: 40 outliers final: 23 residues processed: 242 average time/residue: 0.7409 time to fit residues: 196.9378 Evaluate side-chains 241 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 193 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114526 restraints weight = 13106.732| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 0.83 r_work: 0.3221 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 16565 Z= 0.157 Angle : 0.697 29.170 22329 Z= 0.325 Chirality : 0.044 0.144 2326 Planarity : 0.004 0.058 2884 Dihedral : 6.087 69.484 2525 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.36 % Allowed : 13.11 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1988 helix: 1.39 (0.16), residues: 992 sheet: -0.57 (0.36), residues: 199 loop : -0.29 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.018 0.002 TYR A 229 PHE 0.013 0.001 PHE C 409 TRP 0.019 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00321 (16549) covalent geometry : angle 0.69736 (22329) hydrogen bonds : bond 0.04438 ( 780) hydrogen bonds : angle 5.50242 ( 2256) Misc. bond : bond 0.08327 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.584 Fit side-chains REVERT: A 7 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5349 (t70) REVERT: A 11 SER cc_start: 0.6540 (m) cc_final: 0.6286 (p) REVERT: A 26 LYS cc_start: 0.7393 (mttt) cc_final: 0.6657 (mmtm) REVERT: A 168 LYS cc_start: 0.8549 (mttt) cc_final: 0.8178 (ttpp) REVERT: A 172 LYS cc_start: 0.8440 (tmtp) cc_final: 0.7736 (tmmt) REVERT: A 217 GLU cc_start: 0.7794 (mm-30) cc_final: 0.6924 (tm-30) REVERT: A 318 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7304 (tm-30) REVERT: A 347 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 392 LYS cc_start: 0.7335 (mptt) cc_final: 0.6109 (pmtt) REVERT: A 415 LYS cc_start: 0.7580 (tppt) cc_final: 0.6939 (tptp) REVERT: A 445 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: A 473 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7940 (mptt) REVERT: A 476 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: B 142 LYS cc_start: 0.8598 (mptt) cc_final: 0.8103 (mmpt) REVERT: C 1 MET cc_start: 0.1760 (tpp) cc_final: 0.0782 (ttm) REVERT: C 26 LYS cc_start: 0.7501 (mttt) cc_final: 0.6781 (mmtm) REVERT: C 172 LYS cc_start: 0.8179 (tttt) cc_final: 0.7765 (tmmt) REVERT: C 176 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7969 (mtpp) REVERT: C 217 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7324 (tm-30) REVERT: C 287 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: C 345 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7278 (mtp180) REVERT: C 347 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: C 392 LYS cc_start: 0.7237 (mptp) cc_final: 0.6165 (pmtt) REVERT: C 415 LYS cc_start: 0.7543 (tptp) cc_final: 0.6952 (tptp) REVERT: C 445 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: C 473 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7893 (mptt) REVERT: C 476 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: D 142 LYS cc_start: 0.8652 (mttp) cc_final: 0.8163 (mmpt) REVERT: D 237 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8653 (mtt180) REVERT: D 400 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7897 (mtp-110) outliers start: 41 outliers final: 26 residues processed: 238 average time/residue: 0.7567 time to fit residues: 197.6457 Evaluate side-chains 245 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113836 restraints weight = 13069.521| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.83 r_work: 0.3210 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 16565 Z= 0.170 Angle : 0.709 29.208 22329 Z= 0.332 Chirality : 0.045 0.145 2326 Planarity : 0.004 0.061 2884 Dihedral : 6.112 69.025 2523 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 13.11 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.71 (0.19), residues: 1988 helix: 1.36 (0.16), residues: 992 sheet: -0.56 (0.36), residues: 199 loop : -0.29 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.018 0.002 TYR A 229 PHE 0.014 0.002 PHE C 409 TRP 0.018 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00349 (16549) covalent geometry : angle 0.70884 (22329) hydrogen bonds : bond 0.04605 ( 780) hydrogen bonds : angle 5.53187 ( 2256) Misc. bond : bond 0.08869 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.629 Fit side-chains REVERT: A 7 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5425 (t70) REVERT: A 11 SER cc_start: 0.6625 (m) cc_final: 0.6391 (p) REVERT: A 26 LYS cc_start: 0.7408 (mttt) cc_final: 0.6672 (mmtm) REVERT: A 168 LYS cc_start: 0.8558 (mttt) cc_final: 0.8184 (ttpp) REVERT: A 172 LYS cc_start: 0.8456 (tmtp) cc_final: 0.7756 (tmmt) REVERT: A 217 GLU cc_start: 0.7789 (mm-30) cc_final: 0.6925 (tm-30) REVERT: A 318 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7303 (tm-30) REVERT: A 347 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 392 LYS cc_start: 0.7322 (mptt) cc_final: 0.6095 (pmtt) REVERT: A 415 LYS cc_start: 0.7565 (tppt) cc_final: 0.6927 (tptp) REVERT: A 445 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: A 473 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7948 (mptt) REVERT: A 476 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: B 142 LYS cc_start: 0.8601 (mptt) cc_final: 0.8087 (mmpt) REVERT: C 1 MET cc_start: 0.1919 (tpp) cc_final: 0.0901 (ttm) REVERT: C 26 LYS cc_start: 0.7514 (mttt) cc_final: 0.6798 (mmtm) REVERT: C 172 LYS cc_start: 0.8197 (tttt) cc_final: 0.7761 (tmmt) REVERT: C 176 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7971 (mtpp) REVERT: C 217 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7306 (tm-30) REVERT: C 287 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: C 345 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7279 (mtp180) REVERT: C 347 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: C 392 LYS cc_start: 0.7227 (mptp) cc_final: 0.6150 (pmtt) REVERT: C 415 LYS cc_start: 0.7529 (tptp) cc_final: 0.6904 (tptp) REVERT: C 445 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: C 473 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7881 (mptt) REVERT: C 476 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: D 142 LYS cc_start: 0.8640 (mttp) cc_final: 0.8156 (mmpt) REVERT: D 237 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8685 (mtt180) REVERT: D 400 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7899 (mtp-110) outliers start: 39 outliers final: 23 residues processed: 235 average time/residue: 0.7734 time to fit residues: 198.9864 Evaluate side-chains 240 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 187 optimal weight: 0.0670 chunk 152 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115014 restraints weight = 13097.265| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.82 r_work: 0.3227 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16565 Z= 0.153 Angle : 0.698 29.151 22329 Z= 0.324 Chirality : 0.044 0.143 2326 Planarity : 0.004 0.054 2884 Dihedral : 6.041 68.366 2523 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 13.51 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.75 (0.19), residues: 1988 helix: 1.40 (0.16), residues: 992 sheet: -0.58 (0.36), residues: 199 loop : -0.27 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.018 0.002 TYR A 229 PHE 0.016 0.001 PHE C 409 TRP 0.020 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00312 (16549) covalent geometry : angle 0.69801 (22329) hydrogen bonds : bond 0.04363 ( 780) hydrogen bonds : angle 5.48376 ( 2256) Misc. bond : bond 0.08167 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.702 Fit side-chains REVERT: A 7 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5365 (t70) REVERT: A 11 SER cc_start: 0.6602 (m) cc_final: 0.6375 (p) REVERT: A 26 LYS cc_start: 0.7399 (mttt) cc_final: 0.6672 (mmtm) REVERT: A 168 LYS cc_start: 0.8545 (mttt) cc_final: 0.8177 (ttpp) REVERT: A 172 LYS cc_start: 0.8437 (tmtp) cc_final: 0.7724 (tmmt) REVERT: A 217 GLU cc_start: 0.7783 (mm-30) cc_final: 0.6911 (tm-30) REVERT: A 318 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7305 (tm-30) REVERT: A 347 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: A 392 LYS cc_start: 0.7327 (mptt) cc_final: 0.6093 (pmtt) REVERT: A 415 LYS cc_start: 0.7588 (tppt) cc_final: 0.6946 (tptp) REVERT: A 445 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: A 473 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7922 (mptt) REVERT: A 476 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: B 142 LYS cc_start: 0.8591 (mptt) cc_final: 0.8072 (mmpt) REVERT: C 1 MET cc_start: 0.1829 (tpp) cc_final: 0.0887 (ttm) REVERT: C 26 LYS cc_start: 0.7512 (mttt) cc_final: 0.6793 (mmtm) REVERT: C 172 LYS cc_start: 0.8195 (tttt) cc_final: 0.7756 (tmmt) REVERT: C 176 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8000 (mttp) REVERT: C 217 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7307 (tm-30) REVERT: C 287 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: C 345 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7286 (mtp180) REVERT: C 392 LYS cc_start: 0.7245 (mptp) cc_final: 0.6171 (pmtt) REVERT: C 415 LYS cc_start: 0.7523 (tptp) cc_final: 0.6898 (tptp) REVERT: C 445 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: C 473 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7869 (mptt) REVERT: C 476 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: D 142 LYS cc_start: 0.8644 (mttp) cc_final: 0.8163 (mmpt) REVERT: D 237 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8666 (mtt180) REVERT: D 400 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7910 (mtp-110) outliers start: 36 outliers final: 24 residues processed: 231 average time/residue: 0.7815 time to fit residues: 198.0444 Evaluate side-chains 240 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 98 ASN B 135 GLN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108330 restraints weight = 13048.309| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.82 r_work: 0.3148 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.255 16565 Z= 0.325 Angle : 0.841 29.570 22329 Z= 0.411 Chirality : 0.053 0.207 2326 Planarity : 0.005 0.099 2884 Dihedral : 6.494 71.775 2523 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.01 % Allowed : 13.63 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.43 (0.18), residues: 1988 helix: 0.99 (0.16), residues: 1010 sheet: -0.52 (0.37), residues: 193 loop : -0.30 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 96 TYR 0.024 0.003 TYR B 414 PHE 0.023 0.003 PHE C 431 TRP 0.018 0.003 TRP C 472 HIS 0.007 0.002 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00704 (16549) covalent geometry : angle 0.84115 (22329) hydrogen bonds : bond 0.06175 ( 780) hydrogen bonds : angle 5.87502 ( 2256) Misc. bond : bond 0.12113 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.643 Fit side-chains REVERT: A 7 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5204 (t70) REVERT: A 26 LYS cc_start: 0.7486 (mttt) cc_final: 0.6737 (mmtm) REVERT: A 168 LYS cc_start: 0.8589 (mttt) cc_final: 0.8216 (ttpp) REVERT: A 172 LYS cc_start: 0.8495 (tmtp) cc_final: 0.7762 (tmmt) REVERT: A 318 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7383 (tm-30) REVERT: A 347 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: A 415 LYS cc_start: 0.7611 (tppt) cc_final: 0.6958 (tptp) REVERT: A 473 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8037 (mptt) REVERT: A 476 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 142 LYS cc_start: 0.8658 (mptt) cc_final: 0.8146 (mmpt) REVERT: C 1 MET cc_start: 0.1913 (tpp) cc_final: 0.0918 (ttm) REVERT: C 26 LYS cc_start: 0.7577 (mttt) cc_final: 0.6834 (mmtm) REVERT: C 172 LYS cc_start: 0.8287 (tttt) cc_final: 0.7828 (tmmt) REVERT: C 217 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7377 (tm-30) REVERT: C 345 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7250 (mtp180) REVERT: C 445 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: C 473 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7986 (mptt) REVERT: C 476 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: D 142 LYS cc_start: 0.8703 (mttp) cc_final: 0.8178 (mmpt) REVERT: D 400 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7928 (mtp-110) outliers start: 35 outliers final: 20 residues processed: 224 average time/residue: 0.7706 time to fit residues: 189.3098 Evaluate side-chains 229 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 267 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 137 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 247 ASN B 395 ASN D 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114709 restraints weight = 13107.100| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 0.82 r_work: 0.3222 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 16565 Z= 0.152 Angle : 0.709 29.032 22329 Z= 0.331 Chirality : 0.044 0.141 2326 Planarity : 0.004 0.047 2884 Dihedral : 6.166 72.553 2523 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.67 % Allowed : 13.97 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.11 % 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: 0.61 (0.18), residues: 1988 helix: 1.28 (0.16), residues: 996 sheet: -0.59 (0.36), residues: 199 loop : -0.36 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 97 TYR 0.020 0.002 TYR A 229 PHE 0.019 0.001 PHE C 409 TRP 0.025 0.002 TRP C 253 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00308 (16549) covalent geometry : angle 0.70880 (22329) hydrogen bonds : bond 0.04405 ( 780) hydrogen bonds : angle 5.56245 ( 2256) Misc. bond : bond 0.08113 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.39 seconds wall clock time: 119 minutes 7.00 seconds (7147.00 seconds total)