Starting phenix.real_space_refine on Thu Jun 4 16:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xur_67274/06_2026/9xur_67274.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 52 5.16 5 C 8750 2.51 5 N 2358 2.21 5 O 2696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13872 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3407 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 419} Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3407 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 419} Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 1, '3PG': 1, 'ADQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 1, '3PG': 1, 'ADQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 1, '3PG': 1, 'ADQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 1, '3PG': 1, 'ADQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.51, per 1000 atoms: 0.25 Number of scatterers: 13872 At special positions: 0 Unit cell: (106.248, 110.908, 115.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 12 15.00 Mg 4 11.99 O 2696 8.00 N 2358 7.00 C 8750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS C 81 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 528.5 milliseconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 25 sheets defined 29.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.763A pdb=" N PHE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.756A pdb=" N ILE A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.719A pdb=" N GLU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.802A pdb=" N PHE B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.613A pdb=" N LYS B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 196 through 202 removed outlier: 3.859A pdb=" N GLU C 202 " --> pdb=" O TRP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.850A pdb=" N PHE C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 279 through 284 removed outlier: 4.024A pdb=" N ILE C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.770A pdb=" N GLU C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 352 through 363 removed outlier: 3.798A pdb=" N ILE C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 189 through 196 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 224 through 236 removed outlier: 3.829A pdb=" N PHE D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.507A pdb=" N LYS D 278 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 310 through 319 Processing helix chain 'D' and resid 330 through 339 removed outlier: 4.640A pdb=" N LYS D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 3.529A pdb=" N LEU D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.795A pdb=" N ILE A 139 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU A 174 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 141 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS A 138 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA A 212 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLY A 300 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA A 238 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 301 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 236 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 254 removed outlier: 3.709A pdb=" N GLU A 263 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.165A pdb=" N LYS A 391 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 407 " --> pdb=" O ILE A 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 424 current: chain 'B' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 414 through 416 current: chain 'B' and resid 431 through 439 removed outlier: 7.078A pdb=" N LEU B 432 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN B 469 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 434 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 471 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 467 " --> pdb=" O ILE B 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 484 through 485 current: chain 'B' and resid 501 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 494 removed outlier: 6.789A pdb=" N ILE A 470 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 417 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 401 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS B 393 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE B 409 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.308A pdb=" N ILE A 429 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 482 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 459 through 460 removed outlier: 5.497A pdb=" N GLY A 459 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 476 " --> pdb=" O ILE A 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 95 removed outlier: 4.876A pdb=" N LYS B 138 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 139 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 173 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 141 " --> pdb=" O LEU B 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 174 current: chain 'B' and resid 265 through 270 Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB2, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB3, first strand: chain 'B' and resid 461 through 462 removed outlier: 5.597A pdb=" N GLY B 461 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 478 " --> pdb=" O ILE B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.769A pdb=" N ILE C 139 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU C 174 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C 141 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS C 138 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA C 212 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLY C 300 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 238 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 301 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 236 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB7, first strand: chain 'C' and resid 252 through 254 removed outlier: 3.980A pdb=" N GLU C 263 " --> pdb=" O LYS C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.164A pdb=" N LYS C 391 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 407 " --> pdb=" O ILE C 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 423 through 424 current: chain 'D' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 416 current: chain 'D' and resid 431 through 437 removed outlier: 6.347A pdb=" N GLN D 431 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLU D 470 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LYS D 433 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE D 472 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N THR D 435 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 467 " --> pdb=" O ILE D 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 484 through 485 current: chain 'D' and resid 501 through 503 Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 494 removed outlier: 6.333A pdb=" N LEU C 434 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C 417 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 401 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS D 393 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE D 409 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.377A pdb=" N LYS C 412 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 429 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 482 " --> pdb=" O ILE C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 459 through 460 removed outlier: 5.566A pdb=" N GLY C 459 " --> pdb=" O ILE C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 174 removed outlier: 6.451A pdb=" N VAL D 139 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 173 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 141 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS D 138 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER D 216 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY D 304 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER D 242 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 305 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER D 240 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AC5, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AC6, first strand: chain 'D' and resid 255 through 258 removed outlier: 3.664A pdb=" N SER D 267 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 461 through 462 removed outlier: 5.572A pdb=" N GLY D 461 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG D 478 " --> pdb=" O ILE D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 392 hydrogen bonds defined for protein. 1026 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: 2.31 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4588 1.34 - 1.46: 3117 1.46 - 1.58: 6333 1.58 - 1.70: 20 1.70 - 1.82: 86 Bond restraints: 14144 Sorted by residual: bond pdb=" O3B ADQ D 602 " pdb=" PB ADQ D 602 " ideal model delta sigma weight residual 1.655 1.583 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O3B ADQ A 602 " pdb=" PB ADQ A 602 " ideal model delta sigma weight residual 1.655 1.583 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O3B ADQ C 602 " pdb=" PB ADQ C 602 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O5D ADQ A 602 " pdb=" PA ADQ A 602 " ideal model delta sigma weight residual 1.649 1.581 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3B ADQ B 602 " pdb=" PB ADQ B 602 " ideal model delta sigma weight residual 1.655 1.588 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 14139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 18863 2.08 - 4.15: 231 4.15 - 6.23: 55 6.23 - 8.31: 20 8.31 - 10.39: 9 Bond angle restraints: 19178 Sorted by residual: angle pdb=" O3A ADQ D 602 " pdb=" PB ADQ D 602 " pdb=" O3B ADQ D 602 " ideal model delta sigma weight residual 93.67 104.06 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O3A ADQ A 602 " pdb=" PB ADQ A 602 " pdb=" O3B ADQ A 602 " ideal model delta sigma weight residual 93.67 103.87 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CB MET C 162 " pdb=" CG MET C 162 " pdb=" SD MET C 162 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N GLY D 162 " pdb=" CA GLY D 162 " pdb=" C GLY D 162 " ideal model delta sigma weight residual 115.32 111.38 3.94 1.31e+00 5.83e-01 9.04e+00 angle pdb=" C2 ADQ C 602 " pdb=" N3 ADQ C 602 " pdb=" C4 ADQ C 602 " ideal model delta sigma weight residual 111.57 120.50 -8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 19173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7494 17.86 - 35.72: 819 35.72 - 53.58: 240 53.58 - 71.44: 91 71.44 - 89.30: 25 Dihedral angle restraints: 8669 sinusoidal: 3609 harmonic: 5060 Sorted by residual: dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N LYS B 309 " pdb=" CA LYS B 309 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG D 386 " pdb=" C ARG D 386 " pdb=" N ARG D 387 " pdb=" CA ARG D 387 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG B 386 " pdb=" C ARG B 386 " pdb=" N ARG B 387 " pdb=" CA ARG B 387 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 8666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1629 0.049 - 0.098: 330 0.098 - 0.148: 180 0.148 - 0.197: 1 0.197 - 0.246: 4 Chirality restraints: 2144 Sorted by residual: chirality pdb=" C2D ADQ D 602 " pdb=" C1D ADQ D 602 " pdb=" C3D ADQ D 602 " pdb=" O2D ADQ D 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2D ADQ A 602 " pdb=" C1D ADQ A 602 " pdb=" C3D ADQ A 602 " pdb=" O2D ADQ A 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C2D ADQ B 602 " pdb=" C1D ADQ B 602 " pdb=" C3D ADQ B 602 " pdb=" O2D ADQ B 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2141 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 244 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO D 245 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 284 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.45e+00 pdb=" C THR D 284 " -0.021 2.00e-02 2.50e+03 pdb=" O THR D 284 " 0.008 2.00e-02 2.50e+03 pdb=" N THR D 285 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 368 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 369 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " -0.016 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 15 2.49 - 3.09: 9614 3.09 - 3.69: 20980 3.69 - 4.30: 33868 4.30 - 4.90: 54903 Nonbonded interactions: 119380 Sorted by model distance: nonbonded pdb=" O1B ADQ B 602 " pdb="MG MG B 603 " model vdw 1.886 2.170 nonbonded pdb=" O1B ADQ D 602 " pdb="MG MG D 603 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP D 218 " pdb="MG MG D 603 " model vdw 1.992 2.170 nonbonded pdb=" OD2 ASP B 218 " pdb="MG MG B 603 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP A 214 " pdb="MG MG A 603 " model vdw 2.013 2.170 ... (remaining 119375 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.004 0.072 14145 Z= 0.202 Angle : 0.643 10.385 19180 Z= 0.285 Chirality : 0.048 0.246 2144 Planarity : 0.003 0.031 2464 Dihedral : 17.703 89.303 5434 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.91 % Allowed : 19.21 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1750 helix: 0.14 (0.27), residues: 376 sheet: -0.27 (0.31), residues: 302 loop : -0.01 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.015 0.001 TYR C 165 PHE 0.012 0.001 PHE B 334 TRP 0.005 0.001 TRP B 186 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (14144) covalent geometry : angle 0.64351 / 0.29 (19178) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.20047 / 0.12 ( 2) hydrogen bonds : bond 0.18525 / 12.12 ( 392) hydrogen bonds : angle 8.17870 / 5.82 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.565 Fit side-chains REVERT: A 181 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 220 ASP cc_start: 0.8182 (t70) cc_final: 0.7958 (t0) REVERT: A 325 SER cc_start: 0.7841 (t) cc_final: 0.7606 (p) REVERT: A 342 LEU cc_start: 0.7777 (mm) cc_final: 0.7531 (mt) REVERT: A 344 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: A 348 GLU cc_start: 0.7633 (tp30) cc_final: 0.7107 (tt0) REVERT: A 482 LYS cc_start: 0.7737 (mtpt) cc_final: 0.6974 (mtmt) REVERT: B 156 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.7952 (mtt180) REVERT: B 203 ASP cc_start: 0.7643 (t70) cc_final: 0.7301 (t70) REVERT: B 205 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.7652 (ptp-170) REVERT: B 208 ASP cc_start: 0.8119 (m-30) cc_final: 0.7823 (m-30) REVERT: B 224 ASP cc_start: 0.8376 (t0) cc_final: 0.8012 (t0) REVERT: B 253 ASP cc_start: 0.7493 (m-30) cc_final: 0.7175 (m-30) REVERT: B 289 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.5113 (pp) REVERT: B 311 GLU cc_start: 0.7696 (pm20) cc_final: 0.7343 (pm20) REVERT: B 326 ASP cc_start: 0.7698 (t70) cc_final: 0.6999 (t0) REVERT: B 337 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7061 (mppt) REVERT: B 340 TYR cc_start: 0.8048 (t80) cc_final: 0.7704 (t80) REVERT: B 393 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7007 (tmtm) REVERT: B 396 ASN cc_start: 0.8114 (t0) cc_final: 0.7865 (t0) REVERT: B 429 ASN cc_start: 0.8050 (m-40) cc_final: 0.7172 (m-40) REVERT: B 467 LYS cc_start: 0.7866 (mppt) cc_final: 0.6925 (mptp) REVERT: B 517 LYS cc_start: 0.7945 (mttp) cc_final: 0.7518 (mmmt) REVERT: C 156 ARG cc_start: 0.7561 (mtp85) cc_final: 0.6893 (mtm180) REVERT: C 201 GLU cc_start: 0.7150 (tt0) cc_final: 0.6599 (mm-30) REVERT: C 243 ASP cc_start: 0.7376 (p0) cc_final: 0.7138 (p0) REVERT: C 263 GLU cc_start: 0.7356 (tp30) cc_final: 0.7125 (pt0) REVERT: C 306 ARG cc_start: 0.7397 (ttt180) cc_final: 0.6919 (ttt180) REVERT: C 354 GLU cc_start: 0.7809 (tt0) cc_final: 0.7092 (tm-30) REVERT: C 399 ASP cc_start: 0.8204 (m-30) cc_final: 0.7330 (t70) REVERT: C 467 LYS cc_start: 0.8122 (tttt) cc_final: 0.6965 (tmtt) REVERT: C 482 LYS cc_start: 0.7859 (mttt) cc_final: 0.7161 (mptt) REVERT: C 486 SER cc_start: 0.7196 (p) cc_final: 0.6975 (t) REVERT: D 88 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7303 (mtt90) REVERT: D 109 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7657 (mmt90) REVERT: D 185 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (mtp-110) REVERT: D 247 ASP cc_start: 0.8135 (p0) cc_final: 0.7929 (p0) REVERT: D 262 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6987 (pttt) REVERT: D 267 SER cc_start: 0.8140 (t) cc_final: 0.7566 (p) REVERT: D 280 MET cc_start: 0.7280 (mmm) cc_final: 0.6926 (tpt) REVERT: D 416 GLU cc_start: 0.7860 (tt0) cc_final: 0.6905 (tm-30) REVERT: D 429 ASN cc_start: 0.8040 (m-40) cc_final: 0.7489 (m110) REVERT: D 467 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7127 (mptp) REVERT: D 481 LYS cc_start: 0.7681 (pttt) cc_final: 0.7149 (ptpp) REVERT: D 493 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: D 497 SER cc_start: 0.8230 (p) cc_final: 0.7983 (t) outliers start: 28 outliers final: 13 residues processed: 237 average time/residue: 0.6398 time to fit residues: 164.6249 Evaluate side-chains 214 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 161 ASN B 315 ASN B 342 ASN B 457 ASN B 469 GLN C 177 GLN C 383 GLN D 159 ASN D 230 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100410 restraints weight = 15668.079| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.83 r_work: 0.3062 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14145 Z= 0.214 Angle : 0.579 7.717 19180 Z= 0.302 Chirality : 0.051 0.182 2144 Planarity : 0.004 0.034 2464 Dihedral : 11.644 89.681 2228 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.34 % Allowed : 16.96 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1750 helix: 0.12 (0.26), residues: 398 sheet: -0.55 (0.28), residues: 326 loop : -0.19 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 337 TYR 0.016 0.002 TYR C 165 PHE 0.013 0.002 PHE D 308 TRP 0.004 0.001 TRP D 199 HIS 0.009 0.002 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (14144) covalent geometry : angle 0.57938 / 0.30 (19178) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 0.35225 / 0.20 ( 2) hydrogen bonds : bond 0.04266 / 2.86 ( 392) hydrogen bonds : angle 6.25451 / 4.52 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.577 Fit side-chains REVERT: A 181 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 232 ASP cc_start: 0.6849 (t70) cc_final: 0.6615 (m-30) REVERT: A 342 LEU cc_start: 0.8328 (mm) cc_final: 0.8066 (mt) REVERT: A 348 GLU cc_start: 0.8416 (tp30) cc_final: 0.7858 (tt0) REVERT: A 482 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8011 (mtmt) REVERT: A 494 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7218 (mmm160) REVERT: B 156 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: B 205 ARG cc_start: 0.8497 (ptp-170) cc_final: 0.8144 (ptp-170) REVERT: B 224 ASP cc_start: 0.8763 (t0) cc_final: 0.8559 (t0) REVERT: B 253 ASP cc_start: 0.8016 (m-30) cc_final: 0.7724 (m-30) REVERT: B 262 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6660 (mmmm) REVERT: B 289 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5461 (pp) REVERT: B 303 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: B 311 GLU cc_start: 0.8055 (pm20) cc_final: 0.7743 (pm20) REVERT: B 326 ASP cc_start: 0.8323 (t70) cc_final: 0.7974 (t0) REVERT: B 337 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7587 (mppt) REVERT: B 340 TYR cc_start: 0.8522 (t80) cc_final: 0.8199 (t80) REVERT: B 380 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (ptpp) REVERT: B 393 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8015 (tmtm) REVERT: B 429 ASN cc_start: 0.8534 (m-40) cc_final: 0.8196 (m-40) REVERT: B 467 LYS cc_start: 0.8508 (mppt) cc_final: 0.7981 (mptp) REVERT: B 517 LYS cc_start: 0.8609 (mttp) cc_final: 0.8313 (mmmt) REVERT: C 117 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8554 (tp) REVERT: C 156 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7682 (mtt-85) REVERT: C 201 GLU cc_start: 0.7853 (tt0) cc_final: 0.7325 (mm-30) REVERT: C 243 ASP cc_start: 0.7952 (p0) cc_final: 0.7701 (p0) REVERT: C 277 LYS cc_start: 0.7425 (mttt) cc_final: 0.7082 (mttp) REVERT: C 306 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7715 (ttt180) REVERT: C 354 GLU cc_start: 0.8387 (tt0) cc_final: 0.7951 (tt0) REVERT: C 482 LYS cc_start: 0.8401 (mttt) cc_final: 0.7977 (mmtt) REVERT: C 491 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: D 88 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8109 (mtt90) REVERT: D 109 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8167 (mmt90) REVERT: D 262 LYS cc_start: 0.7624 (ptpp) cc_final: 0.7243 (pttt) REVERT: D 267 SER cc_start: 0.8311 (t) cc_final: 0.7875 (p) REVERT: D 280 MET cc_start: 0.8311 (mmm) cc_final: 0.8016 (tpt) REVERT: D 399 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9040 (mt) REVERT: D 416 GLU cc_start: 0.8449 (tt0) cc_final: 0.7938 (tm-30) REVERT: D 467 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8119 (mptp) REVERT: D 481 LYS cc_start: 0.8532 (pttt) cc_final: 0.8174 (ptpp) outliers start: 49 outliers final: 21 residues processed: 228 average time/residue: 0.6526 time to fit residues: 161.5799 Evaluate side-chains 214 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 464 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 316 GLN B 342 ASN B 457 ASN B 469 GLN C 383 GLN D 159 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103191 restraints weight = 15908.695| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.82 r_work: 0.3104 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14145 Z= 0.115 Angle : 0.496 7.987 19180 Z= 0.258 Chirality : 0.047 0.134 2144 Planarity : 0.003 0.034 2464 Dihedral : 10.372 88.526 2207 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.79 % Allowed : 17.64 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1750 helix: 0.38 (0.27), residues: 400 sheet: -0.59 (0.28), residues: 326 loop : -0.14 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.015 0.001 TYR C 165 PHE 0.011 0.001 PHE B 308 TRP 0.005 0.001 TRP A 185 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14144) covalent geometry : angle 0.49572 / 0.26 (19178) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.08642 / 0.05 ( 2) hydrogen bonds : bond 0.03558 / 2.38 ( 392) hydrogen bonds : angle 5.94174 / 4.30 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.535 Fit side-chains REVERT: A 181 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 232 ASP cc_start: 0.6808 (t70) cc_final: 0.6577 (m-30) REVERT: A 342 LEU cc_start: 0.8311 (mm) cc_final: 0.8069 (mt) REVERT: A 348 GLU cc_start: 0.8400 (tp30) cc_final: 0.7836 (tt0) REVERT: A 450 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7006 (mp) REVERT: A 482 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8034 (mtmt) REVERT: B 156 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8492 (mtt180) REVERT: B 205 ARG cc_start: 0.8493 (ptp-170) cc_final: 0.8136 (ptp-170) REVERT: B 224 ASP cc_start: 0.8768 (t0) cc_final: 0.8557 (t0) REVERT: B 253 ASP cc_start: 0.8045 (m-30) cc_final: 0.7747 (m-30) REVERT: B 262 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6581 (mmmm) REVERT: B 303 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8528 (mtm) REVERT: B 311 GLU cc_start: 0.7999 (pm20) cc_final: 0.7710 (pm20) REVERT: B 326 ASP cc_start: 0.8297 (t70) cc_final: 0.7921 (t0) REVERT: B 337 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7601 (mppt) REVERT: B 340 TYR cc_start: 0.8524 (t80) cc_final: 0.8292 (t80) REVERT: B 380 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (ptpp) REVERT: B 393 LYS cc_start: 0.8626 (ttpp) cc_final: 0.7997 (tmtm) REVERT: B 429 ASN cc_start: 0.8530 (m-40) cc_final: 0.7941 (m-40) REVERT: B 467 LYS cc_start: 0.8492 (mppt) cc_final: 0.7989 (mptp) REVERT: B 517 LYS cc_start: 0.8558 (mttp) cc_final: 0.8265 (mmmt) REVERT: C 117 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8479 (tp) REVERT: C 156 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7679 (mtt-85) REVERT: C 201 GLU cc_start: 0.7775 (tt0) cc_final: 0.7270 (mm-30) REVERT: C 243 ASP cc_start: 0.7996 (p0) cc_final: 0.7744 (p0) REVERT: C 306 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7699 (ttt180) REVERT: C 354 GLU cc_start: 0.8366 (tt0) cc_final: 0.7953 (tt0) REVERT: C 410 ASN cc_start: 0.7785 (t0) cc_final: 0.7563 (t0) REVERT: C 482 LYS cc_start: 0.8437 (mttt) cc_final: 0.7998 (mmtt) REVERT: D 88 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8136 (mtt90) REVERT: D 109 ARG cc_start: 0.8375 (mtp180) cc_final: 0.8154 (mmt90) REVERT: D 267 SER cc_start: 0.8309 (t) cc_final: 0.7907 (p) REVERT: D 280 MET cc_start: 0.8294 (mmm) cc_final: 0.7942 (tpt) REVERT: D 399 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8878 (mt) REVERT: D 416 GLU cc_start: 0.8423 (tt0) cc_final: 0.7933 (tm-30) REVERT: D 429 ASN cc_start: 0.8361 (m-40) cc_final: 0.8098 (m110) REVERT: D 467 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8147 (mptp) REVERT: D 481 LYS cc_start: 0.8535 (pttt) cc_final: 0.8209 (ptpp) outliers start: 41 outliers final: 20 residues processed: 222 average time/residue: 0.6176 time to fit residues: 149.1042 Evaluate side-chains 211 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 342 ASN B 406 HIS B 457 ASN B 469 GLN C 383 GLN D 159 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097040 restraints weight = 15196.895| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.84 r_work: 0.2989 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14145 Z= 0.109 Angle : 0.478 6.898 19180 Z= 0.250 Chirality : 0.047 0.135 2144 Planarity : 0.003 0.035 2464 Dihedral : 9.765 89.784 2201 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.59 % Allowed : 17.85 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1750 helix: 0.44 (0.26), residues: 412 sheet: -0.60 (0.28), residues: 326 loop : -0.05 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.015 0.001 TYR C 165 PHE 0.011 0.001 PHE B 360 TRP 0.005 0.001 TRP A 185 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14144) covalent geometry : angle 0.47805 / 0.25 (19178) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.09042 / 0.05 ( 2) hydrogen bonds : bond 0.03292 / 2.20 ( 392) hydrogen bonds : angle 5.71809 / 4.14 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.476 Fit side-chains REVERT: A 181 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 232 ASP cc_start: 0.6709 (t70) cc_final: 0.6409 (m-30) REVERT: A 342 LEU cc_start: 0.8197 (mm) cc_final: 0.7959 (mt) REVERT: A 348 GLU cc_start: 0.8335 (tp30) cc_final: 0.7671 (tt0) REVERT: A 450 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 482 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7874 (mtmt) REVERT: B 156 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8503 (mtt180) REVERT: B 159 ASN cc_start: 0.7565 (p0) cc_final: 0.7225 (t0) REVERT: B 161 ASN cc_start: 0.8066 (m-40) cc_final: 0.7831 (m110) REVERT: B 205 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.8211 (ptp-170) REVERT: B 224 ASP cc_start: 0.8733 (t0) cc_final: 0.8440 (t0) REVERT: B 253 ASP cc_start: 0.7968 (m-30) cc_final: 0.7588 (m-30) REVERT: B 262 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6546 (mmmm) REVERT: B 303 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8596 (mtm) REVERT: B 311 GLU cc_start: 0.7913 (pm20) cc_final: 0.7609 (pm20) REVERT: B 326 ASP cc_start: 0.8244 (t70) cc_final: 0.7763 (t0) REVERT: B 337 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7449 (mppt) REVERT: B 340 TYR cc_start: 0.8396 (t80) cc_final: 0.8072 (t80) REVERT: B 380 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: B 393 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8136 (tttt) REVERT: B 429 ASN cc_start: 0.8523 (m-40) cc_final: 0.7826 (m-40) REVERT: B 455 GLU cc_start: 0.6927 (pt0) cc_final: 0.6059 (mp0) REVERT: B 467 LYS cc_start: 0.8426 (mppt) cc_final: 0.7814 (mptp) REVERT: B 517 LYS cc_start: 0.8449 (mttp) cc_final: 0.8132 (mmmt) REVERT: C 117 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 156 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7473 (mtt-85) REVERT: C 201 GLU cc_start: 0.7775 (tt0) cc_final: 0.7106 (mm-30) REVERT: C 243 ASP cc_start: 0.7878 (p0) cc_final: 0.7587 (p0) REVERT: C 306 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7520 (ttt180) REVERT: C 354 GLU cc_start: 0.8257 (tt0) cc_final: 0.7755 (tm-30) REVERT: C 482 LYS cc_start: 0.8409 (mttt) cc_final: 0.7845 (mmtt) REVERT: C 486 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.7219 (t) REVERT: D 88 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7979 (mtt90) REVERT: D 109 ARG cc_start: 0.8335 (mtp180) cc_final: 0.8083 (mmt90) REVERT: D 267 SER cc_start: 0.8266 (t) cc_final: 0.7787 (p) REVERT: D 280 MET cc_start: 0.8144 (mmm) cc_final: 0.7861 (tpt) REVERT: D 399 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8899 (mt) REVERT: D 416 GLU cc_start: 0.8397 (tt0) cc_final: 0.7756 (tm-30) REVERT: D 429 ASN cc_start: 0.8385 (m-40) cc_final: 0.8049 (m110) REVERT: D 467 LYS cc_start: 0.8686 (mtmt) cc_final: 0.7988 (mptp) REVERT: D 481 LYS cc_start: 0.8413 (pttt) cc_final: 0.8016 (ptpp) REVERT: D 493 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (mm-30) outliers start: 38 outliers final: 19 residues processed: 217 average time/residue: 0.6445 time to fit residues: 151.9257 Evaluate side-chains 212 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 342 ASN B 469 GLN C 177 GLN C 383 GLN C 410 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101164 restraints weight = 15893.679| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.82 r_work: 0.3067 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14145 Z= 0.191 Angle : 0.554 7.785 19180 Z= 0.289 Chirality : 0.050 0.175 2144 Planarity : 0.004 0.036 2464 Dihedral : 10.227 88.620 2200 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.61 % Allowed : 17.17 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1750 helix: 0.25 (0.26), residues: 412 sheet: -0.75 (0.27), residues: 326 loop : -0.15 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.016 0.002 TYR C 165 PHE 0.013 0.002 PHE B 360 TRP 0.005 0.001 TRP C 347 HIS 0.009 0.002 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (14144) covalent geometry : angle 0.55384 / 0.29 (19178) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.23275 / 0.13 ( 2) hydrogen bonds : bond 0.03824 / 2.57 ( 392) hydrogen bonds : angle 5.84229 / 4.24 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.423 Fit side-chains REVERT: A 181 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 232 ASP cc_start: 0.6825 (t70) cc_final: 0.6513 (m-30) REVERT: A 285 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.3909 (mp) REVERT: A 342 LEU cc_start: 0.8334 (mm) cc_final: 0.8095 (mt) REVERT: A 348 GLU cc_start: 0.8462 (tp30) cc_final: 0.8090 (tp30) REVERT: A 482 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8105 (mtmt) REVERT: B 253 ASP cc_start: 0.8103 (m-30) cc_final: 0.7850 (m-30) REVERT: B 262 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6679 (mmmm) REVERT: B 289 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.5021 (pp) REVERT: B 311 GLU cc_start: 0.8010 (pm20) cc_final: 0.7738 (pm20) REVERT: B 326 ASP cc_start: 0.8306 (t70) cc_final: 0.7907 (t0) REVERT: B 337 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7629 (mppt) REVERT: B 340 TYR cc_start: 0.8537 (t80) cc_final: 0.8172 (t80) REVERT: B 393 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8184 (tttt) REVERT: B 429 ASN cc_start: 0.8626 (m-40) cc_final: 0.8308 (m-40) REVERT: B 467 LYS cc_start: 0.8495 (mppt) cc_final: 0.7983 (mptp) REVERT: B 517 LYS cc_start: 0.8582 (mttp) cc_final: 0.8305 (mmmt) REVERT: C 117 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8567 (tp) REVERT: C 156 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7690 (mtt-85) REVERT: C 201 GLU cc_start: 0.7960 (tt0) cc_final: 0.7264 (mm-30) REVERT: C 243 ASP cc_start: 0.7999 (p0) cc_final: 0.7735 (p0) REVERT: C 260 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7750 (ttt180) REVERT: C 306 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7737 (ttt180) REVERT: C 354 GLU cc_start: 0.8393 (tt0) cc_final: 0.7968 (tm-30) REVERT: C 482 LYS cc_start: 0.8448 (mttt) cc_final: 0.8044 (mmtt) REVERT: C 491 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 88 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8246 (mtm110) REVERT: D 109 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8153 (mmt90) REVERT: D 185 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7710 (mtp-110) REVERT: D 247 ASP cc_start: 0.8589 (p0) cc_final: 0.8361 (p0) REVERT: D 267 SER cc_start: 0.8334 (t) cc_final: 0.7898 (p) REVERT: D 330 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: D 399 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9000 (mt) REVERT: D 416 GLU cc_start: 0.8436 (tt0) cc_final: 0.7936 (tm-30) REVERT: D 467 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8158 (mptp) REVERT: D 481 LYS cc_start: 0.8549 (pttt) cc_final: 0.8205 (ptpp) outliers start: 53 outliers final: 25 residues processed: 220 average time/residue: 0.6609 time to fit residues: 157.5881 Evaluate side-chains 213 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 121 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 342 ASN B 406 HIS B 457 ASN B 469 GLN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099610 restraints weight = 15789.597| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.84 r_work: 0.3048 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14145 Z= 0.224 Angle : 0.576 8.404 19180 Z= 0.302 Chirality : 0.051 0.184 2144 Planarity : 0.004 0.037 2464 Dihedral : 10.551 89.858 2197 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.20 % Allowed : 17.71 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1750 helix: 0.11 (0.26), residues: 412 sheet: -0.85 (0.27), residues: 326 loop : -0.23 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 156 TYR 0.016 0.002 TYR C 165 PHE 0.014 0.002 PHE B 308 TRP 0.005 0.001 TRP C 347 HIS 0.009 0.002 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (14144) covalent geometry : angle 0.57644 / 0.30 (19178) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.20403 / 0.11 ( 2) hydrogen bonds : bond 0.03964 / 2.68 ( 392) hydrogen bonds : angle 5.89277 / 4.28 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.483 Fit side-chains REVERT: A 181 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 232 ASP cc_start: 0.6918 (t70) cc_final: 0.6586 (m-30) REVERT: A 342 LEU cc_start: 0.8342 (mm) cc_final: 0.8116 (mt) REVERT: A 348 GLU cc_start: 0.8468 (tp30) cc_final: 0.8087 (tp30) REVERT: A 482 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8121 (mtmt) REVERT: B 253 ASP cc_start: 0.8129 (m-30) cc_final: 0.7869 (m-30) REVERT: B 262 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6794 (mmmm) REVERT: B 311 GLU cc_start: 0.7965 (pm20) cc_final: 0.7687 (pm20) REVERT: B 326 ASP cc_start: 0.8322 (t70) cc_final: 0.7899 (t0) REVERT: B 337 LYS cc_start: 0.8004 (mmmm) cc_final: 0.7619 (mppt) REVERT: B 340 TYR cc_start: 0.8520 (t80) cc_final: 0.8125 (t80) REVERT: B 393 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8196 (tttt) REVERT: B 429 ASN cc_start: 0.8664 (m-40) cc_final: 0.8341 (m110) REVERT: B 467 LYS cc_start: 0.8502 (mppt) cc_final: 0.7966 (mptp) REVERT: B 517 LYS cc_start: 0.8573 (mttp) cc_final: 0.8283 (mmmt) REVERT: C 117 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8603 (tp) REVERT: C 156 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7673 (mtt180) REVERT: C 201 GLU cc_start: 0.7988 (tt0) cc_final: 0.7362 (mm-30) REVERT: C 243 ASP cc_start: 0.7938 (p0) cc_final: 0.7674 (p0) REVERT: C 260 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: C 306 ARG cc_start: 0.8306 (ttt180) cc_final: 0.7748 (ttt180) REVERT: C 354 GLU cc_start: 0.8390 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 431 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: C 482 LYS cc_start: 0.8441 (mttt) cc_final: 0.8032 (mmtt) REVERT: C 491 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: D 88 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8264 (mtm110) REVERT: D 185 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7621 (mtp-110) REVERT: D 262 LYS cc_start: 0.7678 (ptpp) cc_final: 0.7217 (pttp) REVERT: D 267 SER cc_start: 0.8442 (t) cc_final: 0.7932 (p) REVERT: D 280 MET cc_start: 0.8250 (mmm) cc_final: 0.7943 (tpt) REVERT: D 330 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: D 348 ASP cc_start: 0.8095 (t0) cc_final: 0.7448 (m-30) REVERT: D 399 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9036 (mt) REVERT: D 416 GLU cc_start: 0.8479 (tt0) cc_final: 0.7927 (tm-30) REVERT: D 467 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8109 (mptp) REVERT: D 481 LYS cc_start: 0.8534 (pttt) cc_final: 0.8199 (ptpp) outliers start: 47 outliers final: 23 residues processed: 219 average time/residue: 0.6419 time to fit residues: 152.5091 Evaluate side-chains 213 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 316 GLN B 342 ASN B 457 ASN B 469 GLN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102454 restraints weight = 15752.128| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.81 r_work: 0.3095 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14145 Z= 0.129 Angle : 0.508 7.850 19180 Z= 0.265 Chirality : 0.048 0.143 2144 Planarity : 0.004 0.035 2464 Dihedral : 9.911 89.960 2197 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.52 % Allowed : 18.53 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1750 helix: 0.31 (0.26), residues: 412 sheet: -0.81 (0.27), residues: 326 loop : -0.17 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.015 0.001 TYR C 165 PHE 0.012 0.001 PHE B 360 TRP 0.005 0.001 TRP A 185 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14144) covalent geometry : angle 0.50767 / 0.26 (19178) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.04403 / 0.03 ( 2) hydrogen bonds : bond 0.03407 / 2.28 ( 392) hydrogen bonds : angle 5.73549 / 4.16 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.538 Fit side-chains REVERT: A 156 ARG cc_start: 0.8522 (mtp85) cc_final: 0.7989 (mtm-85) REVERT: A 181 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 232 ASP cc_start: 0.6866 (t70) cc_final: 0.6573 (m-30) REVERT: A 342 LEU cc_start: 0.8326 (mm) cc_final: 0.8106 (mt) REVERT: A 348 GLU cc_start: 0.8448 (tp30) cc_final: 0.8049 (tp30) REVERT: A 450 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7035 (mp) REVERT: A 482 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8102 (mtmt) REVERT: B 253 ASP cc_start: 0.8090 (m-30) cc_final: 0.7826 (m-30) REVERT: B 262 LYS cc_start: 0.7019 (mttp) cc_final: 0.6757 (mmmm) REVERT: B 302 SER cc_start: 0.9002 (p) cc_final: 0.8745 (p) REVERT: B 311 GLU cc_start: 0.8016 (pm20) cc_final: 0.7734 (pm20) REVERT: B 326 ASP cc_start: 0.8264 (t70) cc_final: 0.7814 (t0) REVERT: B 337 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7631 (mppt) REVERT: B 340 TYR cc_start: 0.8523 (t80) cc_final: 0.8234 (t80) REVERT: B 393 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8226 (tttt) REVERT: B 429 ASN cc_start: 0.8665 (m-40) cc_final: 0.8362 (m110) REVERT: B 467 LYS cc_start: 0.8511 (mppt) cc_final: 0.8000 (mptp) REVERT: B 517 LYS cc_start: 0.8545 (mttp) cc_final: 0.8266 (mmmt) REVERT: C 117 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8544 (tp) REVERT: C 156 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7665 (mtt-85) REVERT: C 201 GLU cc_start: 0.7906 (tt0) cc_final: 0.7242 (mm-30) REVERT: C 223 LYS cc_start: 0.8246 (mtmt) cc_final: 0.8007 (mttt) REVERT: C 243 ASP cc_start: 0.7943 (p0) cc_final: 0.7664 (p0) REVERT: C 260 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7358 (ttt180) REVERT: C 306 ARG cc_start: 0.8215 (ttt180) cc_final: 0.7709 (ttt180) REVERT: C 354 GLU cc_start: 0.8382 (tt0) cc_final: 0.7973 (tm-30) REVERT: C 410 ASN cc_start: 0.7736 (t0) cc_final: 0.7506 (t0) REVERT: C 431 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: C 482 LYS cc_start: 0.8431 (mttt) cc_final: 0.8027 (mmtt) REVERT: C 491 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 88 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8225 (mtm110) REVERT: D 267 SER cc_start: 0.8338 (t) cc_final: 0.7889 (p) REVERT: D 280 MET cc_start: 0.8256 (mmm) cc_final: 0.7980 (tpt) REVERT: D 330 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: D 348 ASP cc_start: 0.8087 (t0) cc_final: 0.7457 (m-30) REVERT: D 399 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8890 (mt) REVERT: D 416 GLU cc_start: 0.8443 (tt0) cc_final: 0.7919 (tm-30) REVERT: D 467 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8143 (mptp) REVERT: D 481 LYS cc_start: 0.8537 (pttt) cc_final: 0.8221 (ptpp) REVERT: D 493 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8279 (mm-30) outliers start: 37 outliers final: 23 residues processed: 212 average time/residue: 0.6608 time to fit residues: 151.6890 Evaluate side-chains 212 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 85 optimal weight: 0.0050 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 342 ASN B 457 ASN B 469 GLN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100078 restraints weight = 15763.630| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.85 r_work: 0.3056 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14145 Z= 0.197 Angle : 0.559 8.045 19180 Z= 0.291 Chirality : 0.050 0.177 2144 Planarity : 0.004 0.037 2464 Dihedral : 10.233 89.663 2197 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.86 % Allowed : 18.32 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1750 helix: 0.19 (0.26), residues: 412 sheet: -0.86 (0.27), residues: 326 loop : -0.23 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.016 0.002 TYR C 374 PHE 0.013 0.002 PHE B 360 TRP 0.005 0.001 TRP C 347 HIS 0.008 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (14144) covalent geometry : angle 0.55905 / 0.29 (19178) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.13984 / 0.08 ( 2) hydrogen bonds : bond 0.03790 / 2.55 ( 392) hydrogen bonds : angle 5.81164 / 4.22 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.593 Fit side-chains REVERT: A 168 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5294 (mt-10) REVERT: A 181 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 232 ASP cc_start: 0.6836 (t70) cc_final: 0.6566 (m-30) REVERT: A 342 LEU cc_start: 0.8325 (mm) cc_final: 0.8103 (mt) REVERT: A 348 GLU cc_start: 0.8448 (tp30) cc_final: 0.8057 (tp30) REVERT: A 450 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7124 (mp) REVERT: A 482 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8101 (mtmt) REVERT: B 253 ASP cc_start: 0.8100 (m-30) cc_final: 0.7831 (m-30) REVERT: B 262 LYS cc_start: 0.7101 (mttp) cc_final: 0.6814 (mmmm) REVERT: B 311 GLU cc_start: 0.7995 (pm20) cc_final: 0.7715 (pm20) REVERT: B 326 ASP cc_start: 0.8311 (t70) cc_final: 0.7897 (t0) REVERT: B 337 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7729 (mppt) REVERT: B 340 TYR cc_start: 0.8524 (t80) cc_final: 0.8132 (t80) REVERT: B 393 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8180 (tttt) REVERT: B 429 ASN cc_start: 0.8678 (m-40) cc_final: 0.8353 (m110) REVERT: B 467 LYS cc_start: 0.8491 (mppt) cc_final: 0.7970 (mptp) REVERT: B 517 LYS cc_start: 0.8562 (mttp) cc_final: 0.8276 (mmmt) REVERT: C 117 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8600 (tp) REVERT: C 156 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7656 (mtt-85) REVERT: C 201 GLU cc_start: 0.7986 (tt0) cc_final: 0.7331 (mm-30) REVERT: C 243 ASP cc_start: 0.7939 (p0) cc_final: 0.7669 (p0) REVERT: C 260 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7502 (ttt180) REVERT: C 306 ARG cc_start: 0.8263 (ttt180) cc_final: 0.7714 (ttt180) REVERT: C 354 GLU cc_start: 0.8389 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 410 ASN cc_start: 0.7892 (t0) cc_final: 0.7628 (t0) REVERT: C 431 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: C 482 LYS cc_start: 0.8441 (mttt) cc_final: 0.8029 (mmtt) REVERT: C 491 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 88 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8216 (mtm110) REVERT: D 267 SER cc_start: 0.8435 (t) cc_final: 0.7940 (p) REVERT: D 280 MET cc_start: 0.8224 (mmm) cc_final: 0.7933 (tpt) REVERT: D 330 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: D 348 ASP cc_start: 0.8080 (t0) cc_final: 0.7432 (m-30) REVERT: D 399 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9032 (mt) REVERT: D 416 GLU cc_start: 0.8458 (tt0) cc_final: 0.7908 (tm-30) REVERT: D 467 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8096 (mptp) outliers start: 42 outliers final: 27 residues processed: 206 average time/residue: 0.6329 time to fit residues: 141.7131 Evaluate side-chains 211 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 316 GLN B 342 ASN B 457 ASN B 469 GLN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102621 restraints weight = 15948.452| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.82 r_work: 0.3097 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14145 Z= 0.123 Angle : 0.506 8.335 19180 Z= 0.264 Chirality : 0.048 0.140 2144 Planarity : 0.004 0.035 2464 Dihedral : 9.779 88.992 2197 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.45 % Allowed : 18.66 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1750 helix: 0.38 (0.26), residues: 412 sheet: -0.74 (0.27), residues: 322 loop : -0.18 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 156 TYR 0.016 0.001 TYR C 374 PHE 0.012 0.001 PHE B 360 TRP 0.005 0.001 TRP B 186 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14144) covalent geometry : angle 0.50572 / 0.26 (19178) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.05843 / 0.03 ( 2) hydrogen bonds : bond 0.03335 / 2.23 ( 392) hydrogen bonds : angle 5.71518 / 4.14 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.548 Fit side-chains REVERT: A 168 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.5239 (mt-10) REVERT: A 181 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 232 ASP cc_start: 0.6830 (t70) cc_final: 0.6607 (m-30) REVERT: A 342 LEU cc_start: 0.8327 (mm) cc_final: 0.8105 (mt) REVERT: A 348 GLU cc_start: 0.8455 (tp30) cc_final: 0.8070 (tp30) REVERT: A 450 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 482 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8198 (mtpt) REVERT: B 253 ASP cc_start: 0.8076 (m-30) cc_final: 0.7840 (m-30) REVERT: B 262 LYS cc_start: 0.7045 (mttp) cc_final: 0.6800 (mmmm) REVERT: B 311 GLU cc_start: 0.8015 (pm20) cc_final: 0.7731 (pm20) REVERT: B 326 ASP cc_start: 0.8259 (t70) cc_final: 0.7781 (t0) REVERT: B 337 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7682 (mppt) REVERT: B 340 TYR cc_start: 0.8515 (t80) cc_final: 0.8234 (t80) REVERT: B 429 ASN cc_start: 0.8664 (m-40) cc_final: 0.8363 (m-40) REVERT: B 467 LYS cc_start: 0.8492 (mppt) cc_final: 0.7985 (mptp) REVERT: B 517 LYS cc_start: 0.8534 (mttp) cc_final: 0.8260 (mmmt) REVERT: C 117 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8543 (tp) REVERT: C 156 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7666 (mtt-85) REVERT: C 201 GLU cc_start: 0.7911 (tt0) cc_final: 0.7251 (mm-30) REVERT: C 223 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8016 (mttt) REVERT: C 243 ASP cc_start: 0.7946 (p0) cc_final: 0.7679 (p0) REVERT: C 260 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7439 (ttt180) REVERT: C 306 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7724 (ttt180) REVERT: C 354 GLU cc_start: 0.8392 (tt0) cc_final: 0.7998 (tm-30) REVERT: C 410 ASN cc_start: 0.7740 (t0) cc_final: 0.7514 (t0) REVERT: C 431 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: C 482 LYS cc_start: 0.8433 (mttt) cc_final: 0.8016 (mmtt) REVERT: D 88 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8226 (mtm110) REVERT: D 267 SER cc_start: 0.8330 (t) cc_final: 0.7880 (p) REVERT: D 280 MET cc_start: 0.8233 (mmm) cc_final: 0.7960 (tpt) REVERT: D 330 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: D 348 ASP cc_start: 0.8082 (t0) cc_final: 0.7448 (m-30) REVERT: D 399 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8888 (mt) REVERT: D 416 GLU cc_start: 0.8430 (tt0) cc_final: 0.7903 (tm-30) REVERT: D 467 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8123 (mptp) REVERT: D 481 LYS cc_start: 0.8541 (pttt) cc_final: 0.8225 (ptpp) REVERT: D 493 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8267 (mm-30) outliers start: 36 outliers final: 24 residues processed: 209 average time/residue: 0.6653 time to fit residues: 150.5917 Evaluate side-chains 212 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 9.9990 chunk 166 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 151 optimal weight: 0.0570 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 342 ASN B 457 ASN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103743 restraints weight = 15835.945| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.81 r_work: 0.3114 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14145 Z= 0.110 Angle : 0.492 8.053 19180 Z= 0.256 Chirality : 0.047 0.139 2144 Planarity : 0.003 0.035 2464 Dihedral : 9.423 87.759 2197 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.45 % Allowed : 18.66 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1750 helix: 0.49 (0.26), residues: 412 sheet: -0.69 (0.27), residues: 322 loop : -0.14 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 156 TYR 0.016 0.001 TYR C 165 PHE 0.012 0.001 PHE B 360 TRP 0.006 0.001 TRP B 186 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (14144) covalent geometry : angle 0.49186 / 0.26 (19178) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.02356 / 0.01 ( 2) hydrogen bonds : bond 0.03204 / 2.14 ( 392) hydrogen bonds : angle 5.62105 / 4.08 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.565 Fit side-chains REVERT: A 168 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5237 (mt-10) REVERT: A 181 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 232 ASP cc_start: 0.6803 (t70) cc_final: 0.6601 (m-30) REVERT: A 293 MET cc_start: 0.6627 (mtp) cc_final: 0.6421 (mtm) REVERT: A 342 LEU cc_start: 0.8298 (mm) cc_final: 0.8076 (mt) REVERT: A 348 GLU cc_start: 0.8438 (tp30) cc_final: 0.8040 (tp30) REVERT: A 450 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 482 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8171 (mtpt) REVERT: B 184 LYS cc_start: 0.8060 (mttp) cc_final: 0.7663 (mttt) REVERT: B 253 ASP cc_start: 0.8066 (m-30) cc_final: 0.7832 (m-30) REVERT: B 262 LYS cc_start: 0.7084 (mttp) cc_final: 0.6829 (mmmm) REVERT: B 302 SER cc_start: 0.8997 (p) cc_final: 0.8745 (p) REVERT: B 311 GLU cc_start: 0.8050 (pm20) cc_final: 0.7791 (pm20) REVERT: B 326 ASP cc_start: 0.8255 (t70) cc_final: 0.7782 (t0) REVERT: B 337 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7770 (mppt) REVERT: B 340 TYR cc_start: 0.8528 (t80) cc_final: 0.8220 (t80) REVERT: B 429 ASN cc_start: 0.8674 (m-40) cc_final: 0.8068 (m-40) REVERT: B 467 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8020 (mptp) REVERT: B 517 LYS cc_start: 0.8506 (mttp) cc_final: 0.8233 (mmmt) REVERT: C 117 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8497 (tp) REVERT: C 156 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7669 (mtt-85) REVERT: C 201 GLU cc_start: 0.7870 (tt0) cc_final: 0.7254 (mm-30) REVERT: C 243 ASP cc_start: 0.7962 (p0) cc_final: 0.7695 (p0) REVERT: C 260 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7448 (ttt180) REVERT: C 306 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7663 (ttt180) REVERT: C 354 GLU cc_start: 0.8393 (tt0) cc_final: 0.8007 (tm-30) REVERT: C 410 ASN cc_start: 0.7718 (t0) cc_final: 0.7509 (t0) REVERT: C 431 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: C 482 LYS cc_start: 0.8459 (mttt) cc_final: 0.8033 (mmtt) REVERT: D 88 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8221 (mtm110) REVERT: D 267 SER cc_start: 0.8317 (t) cc_final: 0.7874 (p) REVERT: D 280 MET cc_start: 0.8238 (mmm) cc_final: 0.7887 (tpt) REVERT: D 330 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: D 348 ASP cc_start: 0.7997 (t0) cc_final: 0.7391 (m-30) REVERT: D 399 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8895 (mt) REVERT: D 416 GLU cc_start: 0.8426 (tt0) cc_final: 0.7899 (tm-30) REVERT: D 467 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8120 (mptp) REVERT: D 481 LYS cc_start: 0.8542 (pttt) cc_final: 0.8225 (ptpp) REVERT: D 493 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8249 (mm-30) outliers start: 36 outliers final: 21 residues processed: 214 average time/residue: 0.6480 time to fit residues: 150.4667 Evaluate side-chains 211 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 383 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096273 restraints weight = 15153.223| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.83 r_work: 0.2936 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14145 Z= 0.141 Angle : 0.517 8.253 19180 Z= 0.269 Chirality : 0.048 0.153 2144 Planarity : 0.004 0.035 2464 Dihedral : 9.552 88.672 2197 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.32 % Allowed : 18.80 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1750 helix: 0.44 (0.26), residues: 412 sheet: -0.71 (0.27), residues: 322 loop : -0.16 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.016 0.001 TYR C 165 PHE 0.012 0.001 PHE B 360 TRP 0.006 0.001 TRP A 185 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14144) covalent geometry : angle 0.51731 / 0.27 (19178) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.06688 / 0.04 ( 2) hydrogen bonds : bond 0.03415 / 2.29 ( 392) hydrogen bonds : angle 5.64535 / 4.10 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5265.47 seconds wall clock time: 90 minutes 20.94 seconds (5420.94 seconds total)