Starting phenix.real_space_refine on Fri Jul 3 20:57:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.map" model { file = "/net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ujn_26567/07_2026/7ujn_26567.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 92 5.16 5 C 10288 2.51 5 N 2816 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16272 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "B" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "C" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "D" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.40, per 1000 atoms: 0.21 Number of scatterers: 16272 At special positions: 0 Unit cell: (110.04, 91.56, 118.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 36 15.00 O 3040 8.00 N 2816 7.00 C 10288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 698.7 milliseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 16 sheets defined 59.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.731A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.087A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.630A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 249 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.210A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 5.234A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.670A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.555A pdb=" N ALA A 412 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 414 " --> pdb=" O THR A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.216A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 558 through 576 Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.731A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 4.088A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.637A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.211A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 5.233A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.671A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.555A pdb=" N ALA B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 414 " --> pdb=" O THR B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.216A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.727A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.088A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.634A pdb=" N LEU C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 249 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.211A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 5.233A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.669A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.555A pdb=" N ALA C 412 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE C 413 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 414 " --> pdb=" O THR C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.216A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 558 through 576 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 151 through 156 removed outlier: 3.727A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 4.088A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 215 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.634A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 274 removed outlier: 4.198A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 5.233A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.669A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 394 Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 411 through 414 removed outlier: 3.502A pdb=" N ASP D 414 " --> pdb=" O THR D 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 414' Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.215A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 533 through 537 Processing helix chain 'D' and resid 558 through 576 Processing helix chain 'D' and resid 591 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 343 removed outlier: 8.237A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.888A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 343 removed outlier: 8.238A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.898A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AB1, first strand: chain 'C' and resid 338 through 343 removed outlier: 8.229A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'C' and resid 455 through 460 removed outlier: 6.898A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'D' and resid 338 through 343 removed outlier: 8.237A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 460 removed outlier: 6.901A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 1992 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: 2.82 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5368 1.36 - 1.50: 4270 1.50 - 1.63: 6906 1.63 - 1.77: 0 1.77 - 1.90: 132 Bond restraints: 16676 Sorted by residual: bond pdb=" PA T8T A 702 " pdb=" S1A T8T A 702 " ideal model delta sigma weight residual 2.099 1.898 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" PA T8T C 702 " pdb=" S1A T8T C 702 " ideal model delta sigma weight residual 2.099 1.898 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" PA T8T D 702 " pdb=" S1A T8T D 702 " ideal model delta sigma weight residual 2.099 1.898 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" PA T8T B 701 " pdb=" S1A T8T B 701 " ideal model delta sigma weight residual 2.099 1.898 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" PA T8T A 703 " pdb=" S1A T8T A 703 " ideal model delta sigma weight residual 2.099 1.900 0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 16671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 22286 3.14 - 6.28: 203 6.28 - 9.41: 95 9.41 - 12.55: 20 12.55 - 15.69: 12 Bond angle restraints: 22616 Sorted by residual: angle pdb=" O2A T8T D 702 " pdb=" PA T8T D 702 " pdb=" O3A T8T D 702 " ideal model delta sigma weight residual 121.17 105.48 15.69 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A T8T A 702 " pdb=" PA T8T A 702 " pdb=" O3A T8T A 702 " ideal model delta sigma weight residual 121.17 105.48 15.69 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A T8T C 702 " pdb=" PA T8T C 702 " pdb=" O3A T8T C 702 " ideal model delta sigma weight residual 121.17 105.50 15.67 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A T8T B 701 " pdb=" PA T8T B 701 " pdb=" O3A T8T B 701 " ideal model delta sigma weight residual 121.17 105.52 15.65 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A T8T D 703 " pdb=" PA T8T D 703 " pdb=" O3A T8T D 703 " ideal model delta sigma weight residual 121.17 105.75 15.42 3.00e+00 1.11e-01 2.64e+01 ... (remaining 22611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.60: 9766 28.60 - 57.19: 430 57.19 - 85.79: 80 85.79 - 114.39: 8 114.39 - 142.98: 16 Dihedral angle restraints: 10300 sinusoidal: 4600 harmonic: 5700 Sorted by residual: dihedral pdb=" PB T8T B 702 " pdb=" O3A T8T B 702 " pdb=" PA T8T B 702 " pdb=" S1A T8T B 702 " ideal model delta sinusoidal sigma weight residual -64.84 78.14 -142.98 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" PB T8T D 703 " pdb=" O3A T8T D 703 " pdb=" PA T8T D 703 " pdb=" S1A T8T D 703 " ideal model delta sinusoidal sigma weight residual -64.84 78.13 -142.97 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" PB T8T A 701 " pdb=" O3A T8T A 701 " pdb=" PA T8T A 701 " pdb=" S1A T8T A 701 " ideal model delta sinusoidal sigma weight residual -64.84 78.13 -142.97 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 10297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2376 0.158 - 0.316: 0 0.316 - 0.474: 0 0.474 - 0.632: 0 0.632 - 0.790: 12 Chirality restraints: 2388 Sorted by residual: chirality pdb=" PA T8T D 703 " pdb=" O2A T8T D 703 " pdb=" O3A T8T D 703 " pdb=" O5' T8T D 703 " both_signs ideal model delta sigma weight residual True 2.63 3.42 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PA T8T C 703 " pdb=" O2A T8T C 703 " pdb=" O3A T8T C 703 " pdb=" O5' T8T C 703 " both_signs ideal model delta sigma weight residual True 2.63 3.42 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PA T8T B 702 " pdb=" O2A T8T B 702 " pdb=" O3A T8T B 702 " pdb=" O5' T8T B 702 " both_signs ideal model delta sigma weight residual True 2.63 3.42 -0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 2385 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' T8T B 702 " -0.021 2.00e-02 2.50e+03 9.62e-03 2.54e+00 pdb=" C2 T8T B 702 " 0.004 2.00e-02 2.50e+03 pdb=" C4 T8T B 702 " 0.011 2.00e-02 2.50e+03 pdb=" C5 T8T B 702 " 0.001 2.00e-02 2.50e+03 pdb=" C6 T8T B 702 " -0.010 2.00e-02 2.50e+03 pdb=" C8 T8T B 702 " 0.004 2.00e-02 2.50e+03 pdb=" N1 T8T B 702 " -0.007 2.00e-02 2.50e+03 pdb=" N2 T8T B 702 " -0.004 2.00e-02 2.50e+03 pdb=" N3 T8T B 702 " 0.015 2.00e-02 2.50e+03 pdb=" N7 T8T B 702 " -0.000 2.00e-02 2.50e+03 pdb=" N9 T8T B 702 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' T8T A 701 " -0.021 2.00e-02 2.50e+03 9.59e-03 2.53e+00 pdb=" C2 T8T A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C4 T8T A 701 " 0.011 2.00e-02 2.50e+03 pdb=" C5 T8T A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 T8T A 701 " -0.010 2.00e-02 2.50e+03 pdb=" C8 T8T A 701 " 0.004 2.00e-02 2.50e+03 pdb=" N1 T8T A 701 " -0.008 2.00e-02 2.50e+03 pdb=" N2 T8T A 701 " -0.004 2.00e-02 2.50e+03 pdb=" N3 T8T A 701 " 0.015 2.00e-02 2.50e+03 pdb=" N7 T8T A 701 " -0.000 2.00e-02 2.50e+03 pdb=" N9 T8T A 701 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' T8T D 703 " 0.021 2.00e-02 2.50e+03 9.59e-03 2.53e+00 pdb=" C2 T8T D 703 " -0.004 2.00e-02 2.50e+03 pdb=" C4 T8T D 703 " -0.011 2.00e-02 2.50e+03 pdb=" C5 T8T D 703 " -0.001 2.00e-02 2.50e+03 pdb=" C6 T8T D 703 " 0.010 2.00e-02 2.50e+03 pdb=" C8 T8T D 703 " -0.004 2.00e-02 2.50e+03 pdb=" N1 T8T D 703 " 0.008 2.00e-02 2.50e+03 pdb=" N2 T8T D 703 " 0.004 2.00e-02 2.50e+03 pdb=" N3 T8T D 703 " -0.015 2.00e-02 2.50e+03 pdb=" N7 T8T D 703 " 0.000 2.00e-02 2.50e+03 pdb=" N9 T8T D 703 " -0.007 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 618 2.72 - 3.27: 16176 3.27 - 3.81: 26598 3.81 - 4.36: 34681 4.36 - 4.90: 58096 Nonbonded interactions: 136169 Sorted by model distance: nonbonded pdb=" OD2 ASP B 319 " pdb=" OH TYR B 374 " model vdw 2.175 3.040 nonbonded pdb=" OD2 ASP A 319 " pdb=" OH TYR A 374 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP C 319 " pdb=" OH TYR C 374 " model vdw 2.193 3.040 nonbonded pdb=" OD2 ASP D 319 " pdb=" OH TYR D 374 " model vdw 2.193 3.040 nonbonded pdb=" NZ LYS A 185 " pdb=" O ALA A 338 " model vdw 2.260 3.120 ... (remaining 136164 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.860 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.015 0.584 16684 Z= 1.263 Angle : 0.936 15.688 22616 Z= 0.390 Chirality : 0.071 0.790 2388 Planarity : 0.004 0.034 2884 Dihedral : 17.456 142.981 6636 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.20), residues: 1940 helix: 1.10 (0.18), residues: 884 sheet: -0.24 (0.57), residues: 100 loop : -0.14 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 305 TYR 0.012 0.001 TYR C 315 PHE 0.012 0.001 PHE C 165 TRP 0.013 0.001 TRP D 285 HIS 0.003 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.48 (16676) covalent geometry : angle 0.93632 / 0.39 (22616) hydrogen bonds : bond 0.17449 / 12.00 ( 752) hydrogen bonds : angle 6.20118 / 4.45 ( 1992) Misc. bond : bond 0.53336 / 28.44 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 367 ASN cc_start: 0.7728 (t0) cc_final: 0.7481 (t0) REVERT: A 496 GLU cc_start: 0.7686 (tp30) cc_final: 0.7148 (tt0) REVERT: A 556 LYS cc_start: 0.5610 (mtpt) cc_final: 0.5354 (mtmt) REVERT: B 299 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 367 ASN cc_start: 0.7727 (t0) cc_final: 0.7501 (t0) REVERT: B 496 GLU cc_start: 0.7647 (tp30) cc_final: 0.7143 (tt0) REVERT: B 556 LYS cc_start: 0.5593 (mtpt) cc_final: 0.5359 (mtmt) REVERT: C 299 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 326 GLN cc_start: 0.7334 (mm110) cc_final: 0.6646 (mp10) REVERT: C 367 ASN cc_start: 0.7728 (t0) cc_final: 0.7480 (t0) REVERT: C 496 GLU cc_start: 0.7636 (tp30) cc_final: 0.7138 (tt0) REVERT: D 299 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7538 (mt-10) REVERT: D 326 GLN cc_start: 0.7336 (mm110) cc_final: 0.6656 (mp10) REVERT: D 367 ASN cc_start: 0.7726 (t0) cc_final: 0.7480 (t0) REVERT: D 496 GLU cc_start: 0.7669 (tp30) cc_final: 0.7160 (tt0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.8317 time to fit residues: 206.0749 Evaluate side-chains 159 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 167 HIS A 571 GLN B 119 ASN B 167 HIS C 119 ASN C 167 HIS C 326 GLN D 119 ASN D 167 HIS D 326 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135567 restraints weight = 16520.925| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.47 r_work: 0.3564 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16684 Z= 0.152 Angle : 0.581 6.634 22616 Z= 0.303 Chirality : 0.046 0.155 2388 Planarity : 0.006 0.099 2884 Dihedral : 14.405 127.556 2588 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 7.16 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.19), residues: 1940 helix: 1.00 (0.18), residues: 872 sheet: 0.03 (0.46), residues: 140 loop : -0.42 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 451 TYR 0.037 0.002 TYR C 315 PHE 0.017 0.002 PHE A 213 TRP 0.014 0.001 TRP C 285 HIS 0.005 0.002 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16676) covalent geometry : angle 0.58052 / 0.30 (22616) hydrogen bonds : bond 0.05047 / 3.40 ( 752) hydrogen bonds : angle 5.06135 / 3.70 ( 1992) Misc. bond : bond 0.00073 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7614 (mmmt) REVERT: A 496 GLU cc_start: 0.7830 (tp30) cc_final: 0.7312 (tt0) REVERT: A 531 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7359 (mmt180) REVERT: B 230 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7614 (mmmt) REVERT: B 496 GLU cc_start: 0.7864 (tp30) cc_final: 0.7324 (tt0) REVERT: B 531 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7339 (mmt180) REVERT: C 230 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7600 (mmmt) REVERT: C 326 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7347 (mp10) REVERT: C 496 GLU cc_start: 0.7828 (tp30) cc_final: 0.7288 (tt0) REVERT: C 531 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7362 (mmt180) REVERT: D 230 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7595 (mmmt) REVERT: D 326 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7325 (mp10) REVERT: D 496 GLU cc_start: 0.7839 (tp30) cc_final: 0.7316 (tt0) REVERT: D 531 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7345 (mmt180) outliers start: 37 outliers final: 8 residues processed: 180 average time/residue: 0.8924 time to fit residues: 172.6861 Evaluate side-chains 152 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 531 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 531 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN A 571 GLN B 452 ASN B 571 GLN C 452 ASN C 571 GLN D 452 ASN D 571 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.171053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137304 restraints weight = 16690.898| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.54 r_work: 0.3582 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16684 Z= 0.128 Angle : 0.560 10.895 22616 Z= 0.285 Chirality : 0.045 0.149 2388 Planarity : 0.005 0.090 2884 Dihedral : 13.082 114.656 2588 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.67 % Allowed : 9.30 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.20), residues: 1940 helix: 1.02 (0.18), residues: 872 sheet: 0.00 (0.47), residues: 140 loop : -0.36 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 451 TYR 0.031 0.002 TYR B 315 PHE 0.012 0.002 PHE D 213 TRP 0.012 0.001 TRP C 285 HIS 0.005 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16676) covalent geometry : angle 0.56026 / 0.29 (22616) hydrogen bonds : bond 0.04450 / 3.00 ( 752) hydrogen bonds : angle 4.82129 / 3.53 ( 1992) Misc. bond : bond 0.00288 / 0.14 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.4761 (ttt) REVERT: A 346 GLU cc_start: 0.7849 (pm20) cc_final: 0.7596 (pm20) REVERT: A 496 GLU cc_start: 0.7857 (tp30) cc_final: 0.7322 (tt0) REVERT: A 549 LEU cc_start: 0.7503 (pp) cc_final: 0.7218 (pt) REVERT: B 115 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4740 (ttt) REVERT: B 346 GLU cc_start: 0.7836 (pm20) cc_final: 0.7584 (pm20) REVERT: B 496 GLU cc_start: 0.7854 (tp30) cc_final: 0.7321 (tt0) REVERT: B 549 LEU cc_start: 0.7523 (pp) cc_final: 0.7248 (pt) REVERT: C 115 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.4741 (ttt) REVERT: C 326 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7244 (mp10) REVERT: C 346 GLU cc_start: 0.7838 (pm20) cc_final: 0.7594 (pm20) REVERT: C 496 GLU cc_start: 0.7844 (tp30) cc_final: 0.7274 (tt0) REVERT: C 549 LEU cc_start: 0.7515 (pp) cc_final: 0.7216 (pt) REVERT: D 115 MET cc_start: 0.5452 (OUTLIER) cc_final: 0.4729 (ttt) REVERT: D 326 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7254 (mp10) REVERT: D 346 GLU cc_start: 0.7854 (pm20) cc_final: 0.7609 (pm20) REVERT: D 496 GLU cc_start: 0.7850 (tp30) cc_final: 0.7297 (tt0) REVERT: D 549 LEU cc_start: 0.7507 (pp) cc_final: 0.7216 (pt) outliers start: 29 outliers final: 12 residues processed: 176 average time/residue: 0.8280 time to fit residues: 157.2084 Evaluate side-chains 171 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135631 restraints weight = 16212.868| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.59 r_work: 0.3556 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16684 Z= 0.146 Angle : 0.568 8.374 22616 Z= 0.291 Chirality : 0.046 0.160 2388 Planarity : 0.005 0.075 2884 Dihedral : 12.333 100.222 2588 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.50 % Allowed : 10.45 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.19), residues: 1940 helix: 0.79 (0.18), residues: 896 sheet: -0.14 (0.46), residues: 140 loop : -0.53 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 451 TYR 0.031 0.002 TYR A 315 PHE 0.014 0.002 PHE B 213 TRP 0.012 0.001 TRP D 285 HIS 0.006 0.002 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16676) covalent geometry : angle 0.56769 / 0.29 (22616) hydrogen bonds : bond 0.04681 / 3.16 ( 752) hydrogen bonds : angle 4.81090 / 3.53 ( 1992) Misc. bond : bond 0.00185 / 0.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.4781 (ttt) REVERT: A 240 MET cc_start: 0.8704 (tpp) cc_final: 0.8476 (tpp) REVERT: A 346 GLU cc_start: 0.7853 (pm20) cc_final: 0.7559 (pm20) REVERT: A 496 GLU cc_start: 0.7865 (tp30) cc_final: 0.7326 (pp20) REVERT: A 549 LEU cc_start: 0.7369 (pp) cc_final: 0.7116 (pt) REVERT: B 115 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.4766 (ttt) REVERT: B 240 MET cc_start: 0.8692 (tpp) cc_final: 0.8463 (tpp) REVERT: B 346 GLU cc_start: 0.7824 (pm20) cc_final: 0.7528 (pm20) REVERT: B 496 GLU cc_start: 0.7871 (tp30) cc_final: 0.7317 (pp20) REVERT: B 549 LEU cc_start: 0.7478 (pp) cc_final: 0.7238 (pt) REVERT: C 115 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4772 (ttt) REVERT: C 240 MET cc_start: 0.8703 (tpp) cc_final: 0.8473 (tpp) REVERT: C 326 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7298 (mp10) REVERT: C 346 GLU cc_start: 0.7850 (pm20) cc_final: 0.7588 (pm20) REVERT: C 496 GLU cc_start: 0.7841 (tp30) cc_final: 0.7278 (tt0) REVERT: C 549 LEU cc_start: 0.7386 (pp) cc_final: 0.7133 (pt) REVERT: D 115 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4764 (ttt) REVERT: D 240 MET cc_start: 0.8699 (tpp) cc_final: 0.8470 (tpp) REVERT: D 326 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7297 (mp10) REVERT: D 346 GLU cc_start: 0.7833 (pm20) cc_final: 0.7543 (pm20) REVERT: D 496 GLU cc_start: 0.7849 (tp30) cc_final: 0.7292 (tt0) REVERT: D 549 LEU cc_start: 0.7363 (pp) cc_final: 0.7111 (pt) outliers start: 26 outliers final: 8 residues processed: 184 average time/residue: 0.8335 time to fit residues: 165.4610 Evaluate side-chains 169 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 67 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.168345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133150 restraints weight = 16309.000| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.53 r_work: 0.3520 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16684 Z= 0.206 Angle : 0.637 7.742 22616 Z= 0.326 Chirality : 0.048 0.175 2388 Planarity : 0.005 0.061 2884 Dihedral : 12.739 89.217 2588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.85 % Allowed : 12.41 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.19), residues: 1940 helix: 0.57 (0.18), residues: 872 sheet: -0.14 (0.45), residues: 140 loop : -0.60 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 451 TYR 0.032 0.003 TYR D 315 PHE 0.018 0.002 PHE D 213 TRP 0.013 0.002 TRP C 285 HIS 0.010 0.002 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (16676) covalent geometry : angle 0.63726 / 0.33 (22616) hydrogen bonds : bond 0.05411 / 3.67 ( 752) hydrogen bonds : angle 5.00228 / 3.68 ( 1992) Misc. bond : bond 0.00211 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7505 (p90) REVERT: A 346 GLU cc_start: 0.7725 (pm20) cc_final: 0.7422 (pm20) REVERT: A 496 GLU cc_start: 0.7904 (tp30) cc_final: 0.7381 (pp20) REVERT: A 549 LEU cc_start: 0.7712 (pp) cc_final: 0.7490 (pt) REVERT: B 315 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7503 (p90) REVERT: B 346 GLU cc_start: 0.7698 (pm20) cc_final: 0.7388 (pm20) REVERT: B 496 GLU cc_start: 0.7915 (tp30) cc_final: 0.7385 (pp20) REVERT: B 549 LEU cc_start: 0.7715 (pp) cc_final: 0.7493 (pt) REVERT: C 315 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7511 (p90) REVERT: C 326 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7410 (mp10) REVERT: C 346 GLU cc_start: 0.7703 (pm20) cc_final: 0.7411 (pm20) REVERT: C 496 GLU cc_start: 0.7870 (tp30) cc_final: 0.7319 (tt0) REVERT: C 549 LEU cc_start: 0.7696 (pp) cc_final: 0.7482 (pt) REVERT: D 315 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7500 (p90) REVERT: D 326 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7391 (mp10) REVERT: D 346 GLU cc_start: 0.7695 (pm20) cc_final: 0.7386 (pm20) REVERT: D 496 GLU cc_start: 0.7853 (tp30) cc_final: 0.7291 (tt0) REVERT: D 549 LEU cc_start: 0.7707 (pp) cc_final: 0.7487 (pt) outliers start: 32 outliers final: 12 residues processed: 178 average time/residue: 0.9005 time to fit residues: 172.4232 Evaluate side-chains 162 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.170316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134909 restraints weight = 16181.207| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.54 r_work: 0.3548 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16684 Z= 0.168 Angle : 0.597 7.234 22616 Z= 0.306 Chirality : 0.046 0.165 2388 Planarity : 0.007 0.158 2884 Dihedral : 12.267 88.133 2588 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.31 % Allowed : 13.39 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.19), residues: 1940 helix: 0.53 (0.18), residues: 896 sheet: -0.62 (0.44), residues: 148 loop : -0.61 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 451 TYR 0.031 0.002 TYR B 315 PHE 0.015 0.002 PHE C 363 TRP 0.012 0.001 TRP D 285 HIS 0.007 0.002 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (16676) covalent geometry : angle 0.59739 / 0.31 (22616) hydrogen bonds : bond 0.04888 / 3.30 ( 752) hydrogen bonds : angle 4.86832 / 3.58 ( 1992) Misc. bond : bond 0.00398 / 0.19 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4788 (ttt) REVERT: A 315 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7577 (p90) REVERT: A 346 GLU cc_start: 0.7715 (pm20) cc_final: 0.7387 (pm20) REVERT: A 496 GLU cc_start: 0.7854 (tp30) cc_final: 0.7367 (pp20) REVERT: B 115 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.4809 (ttt) REVERT: B 315 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7589 (p90) REVERT: B 346 GLU cc_start: 0.7676 (pm20) cc_final: 0.7335 (pm20) REVERT: B 496 GLU cc_start: 0.7855 (tp30) cc_final: 0.7381 (pp20) REVERT: B 549 LEU cc_start: 0.7713 (pp) cc_final: 0.7509 (pt) REVERT: C 115 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.4811 (ttt) REVERT: C 315 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7605 (p90) REVERT: C 326 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7378 (mp10) REVERT: C 346 GLU cc_start: 0.7688 (pm20) cc_final: 0.7363 (pm20) REVERT: C 496 GLU cc_start: 0.7836 (tp30) cc_final: 0.7312 (pp20) REVERT: D 115 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4787 (ttt) REVERT: D 315 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7597 (p90) REVERT: D 326 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7368 (mp10) REVERT: D 346 GLU cc_start: 0.7667 (pm20) cc_final: 0.7332 (pm20) REVERT: D 496 GLU cc_start: 0.7822 (tp30) cc_final: 0.7294 (pp20) outliers start: 40 outliers final: 10 residues processed: 182 average time/residue: 0.8165 time to fit residues: 160.7115 Evaluate side-chains 163 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 2.9990 chunk 125 optimal weight: 0.0050 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.170668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135041 restraints weight = 16106.590| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.51 r_work: 0.3563 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16684 Z= 0.160 Angle : 0.590 7.172 22616 Z= 0.304 Chirality : 0.046 0.161 2388 Planarity : 0.006 0.121 2884 Dihedral : 11.081 87.305 2588 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.25 % Allowed : 14.09 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.19), residues: 1940 helix: 0.57 (0.17), residues: 896 sheet: -0.61 (0.44), residues: 148 loop : -0.60 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 451 TYR 0.031 0.002 TYR B 315 PHE 0.015 0.002 PHE D 363 TRP 0.012 0.001 TRP C 285 HIS 0.006 0.001 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (16676) covalent geometry : angle 0.59014 / 0.30 (22616) hydrogen bonds : bond 0.04776 / 3.23 ( 752) hydrogen bonds : angle 4.81855 / 3.55 ( 1992) Misc. bond : bond 0.00312 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4697 (ttt) REVERT: A 220 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: A 315 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7583 (p90) REVERT: A 496 GLU cc_start: 0.7882 (tp30) cc_final: 0.7333 (pp20) REVERT: B 115 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.4729 (ttt) REVERT: B 220 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8074 (mtt180) REVERT: B 315 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7574 (p90) REVERT: B 489 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5774 (mm) REVERT: B 496 GLU cc_start: 0.7840 (tp30) cc_final: 0.7325 (pp20) REVERT: C 115 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.4722 (ttt) REVERT: C 220 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8050 (mtt180) REVERT: C 315 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7610 (p90) REVERT: C 326 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7384 (mp10) REVERT: C 496 GLU cc_start: 0.7846 (tp30) cc_final: 0.7335 (pp20) REVERT: D 115 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.4725 (ttt) REVERT: D 220 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8052 (mtt180) REVERT: D 315 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7590 (p90) REVERT: D 326 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7374 (mp10) REVERT: D 496 GLU cc_start: 0.7834 (tp30) cc_final: 0.7277 (pp20) outliers start: 39 outliers final: 4 residues processed: 172 average time/residue: 0.8804 time to fit residues: 163.5844 Evaluate side-chains 162 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 chunk 102 optimal weight: 8.9990 chunk 39 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.170492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134761 restraints weight = 16206.430| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.51 r_work: 0.3555 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16684 Z= 0.163 Angle : 0.602 12.986 22616 Z= 0.306 Chirality : 0.046 0.163 2388 Planarity : 0.006 0.096 2884 Dihedral : 10.701 87.338 2588 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.96 % Allowed : 14.32 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1940 helix: 0.56 (0.17), residues: 896 sheet: -0.50 (0.45), residues: 148 loop : -0.61 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 451 TYR 0.036 0.002 TYR D 456 PHE 0.015 0.002 PHE C 363 TRP 0.012 0.001 TRP C 285 HIS 0.006 0.002 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (16676) covalent geometry : angle 0.60175 / 0.31 (22616) hydrogen bonds : bond 0.04813 / 3.26 ( 752) hydrogen bonds : angle 4.80824 / 3.54 ( 1992) Misc. bond : bond 0.00270 / 0.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.4634 (ttt) REVERT: A 220 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8058 (mtt180) REVERT: A 315 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7581 (p90) REVERT: A 346 GLU cc_start: 0.7704 (pm20) cc_final: 0.7304 (pm20) REVERT: A 496 GLU cc_start: 0.7884 (tp30) cc_final: 0.7325 (pp20) REVERT: B 115 MET cc_start: 0.5424 (OUTLIER) cc_final: 0.4704 (ttt) REVERT: B 220 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8064 (mtt180) REVERT: B 315 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7565 (p90) REVERT: B 346 GLU cc_start: 0.7662 (pm20) cc_final: 0.7217 (pm20) REVERT: B 496 GLU cc_start: 0.7868 (tp30) cc_final: 0.7313 (pp20) REVERT: C 115 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4691 (ttt) REVERT: C 220 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8040 (mtt180) REVERT: C 315 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7580 (p90) REVERT: C 326 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7393 (mp10) REVERT: C 346 GLU cc_start: 0.7669 (pm20) cc_final: 0.7228 (pm20) REVERT: C 496 GLU cc_start: 0.7859 (tp30) cc_final: 0.7332 (pp20) REVERT: C 549 LEU cc_start: 0.7838 (pp) cc_final: 0.7615 (pt) REVERT: D 115 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4666 (ttt) REVERT: D 220 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8051 (mtt180) REVERT: D 315 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7567 (p90) REVERT: D 326 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7378 (mp10) REVERT: D 346 GLU cc_start: 0.7654 (pm20) cc_final: 0.7257 (pm20) REVERT: D 496 GLU cc_start: 0.7837 (tp30) cc_final: 0.7316 (pp20) REVERT: D 549 LEU cc_start: 0.7785 (pp) cc_final: 0.7561 (pt) outliers start: 34 outliers final: 5 residues processed: 171 average time/residue: 0.9495 time to fit residues: 174.4103 Evaluate side-chains 165 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 136 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 155 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.174522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139055 restraints weight = 16061.584| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.53 r_work: 0.3615 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16684 Z= 0.108 Angle : 0.543 11.911 22616 Z= 0.278 Chirality : 0.044 0.139 2388 Planarity : 0.004 0.060 2884 Dihedral : 9.053 89.259 2588 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.67 % Allowed : 14.95 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1940 helix: 0.91 (0.18), residues: 896 sheet: -0.48 (0.45), residues: 148 loop : -0.42 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 451 TYR 0.037 0.002 TYR C 456 PHE 0.010 0.001 PHE D 213 TRP 0.011 0.001 TRP C 285 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (16676) covalent geometry : angle 0.54344 / 0.28 (22616) hydrogen bonds : bond 0.03827 / 2.58 ( 752) hydrogen bonds : angle 4.54932 / 3.35 ( 1992) Misc. bond : bond 0.00149 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.4653 (ttt) REVERT: A 180 HIS cc_start: 0.7632 (t-90) cc_final: 0.7213 (m-70) REVERT: A 315 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7571 (p90) REVERT: A 346 GLU cc_start: 0.7707 (pm20) cc_final: 0.7305 (pm20) REVERT: A 491 VAL cc_start: 0.5853 (OUTLIER) cc_final: 0.5539 (m) REVERT: A 496 GLU cc_start: 0.7854 (tp30) cc_final: 0.7333 (pp20) REVERT: B 115 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.4665 (ttt) REVERT: B 180 HIS cc_start: 0.7627 (t-90) cc_final: 0.7214 (m-70) REVERT: B 315 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7563 (p90) REVERT: B 346 GLU cc_start: 0.7679 (pm20) cc_final: 0.7276 (pm20) REVERT: B 491 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5567 (m) REVERT: B 496 GLU cc_start: 0.7802 (tp30) cc_final: 0.7298 (pp20) REVERT: C 115 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4666 (ttt) REVERT: C 180 HIS cc_start: 0.7615 (t-90) cc_final: 0.7193 (m-70) REVERT: C 315 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7582 (p90) REVERT: C 326 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7274 (mp10) REVERT: C 344 ASP cc_start: 0.6745 (t0) cc_final: 0.6457 (t0) REVERT: C 346 GLU cc_start: 0.7685 (pm20) cc_final: 0.7285 (pm20) REVERT: C 496 GLU cc_start: 0.7821 (tp30) cc_final: 0.7269 (pp20) REVERT: C 549 LEU cc_start: 0.7498 (pp) cc_final: 0.7241 (pt) REVERT: D 115 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.4683 (ttt) REVERT: D 180 HIS cc_start: 0.7604 (t-90) cc_final: 0.7190 (m-70) REVERT: D 315 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7575 (p90) REVERT: D 326 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7272 (mp10) REVERT: D 346 GLU cc_start: 0.7671 (pm20) cc_final: 0.7270 (pm20) REVERT: D 496 GLU cc_start: 0.7814 (tp30) cc_final: 0.7267 (pp20) REVERT: D 549 LEU cc_start: 0.7495 (pp) cc_final: 0.7236 (pt) outliers start: 29 outliers final: 5 residues processed: 183 average time/residue: 0.8619 time to fit residues: 170.6692 Evaluate side-chains 162 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 0.0270 chunk 187 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN A 571 GLN B 571 GLN C 367 ASN C 425 ASN C 571 GLN D 571 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138597 restraints weight = 16093.564| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.75 r_work: 0.3629 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16684 Z= 0.114 Angle : 0.572 13.083 22616 Z= 0.288 Chirality : 0.044 0.142 2388 Planarity : 0.009 0.217 2884 Dihedral : 8.910 90.481 2588 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.10 % Allowed : 15.76 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.20), residues: 1940 helix: 0.99 (0.18), residues: 896 sheet: -0.39 (0.46), residues: 148 loop : -0.41 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 451 TYR 0.040 0.002 TYR C 456 PHE 0.010 0.001 PHE B 363 TRP 0.011 0.001 TRP C 285 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (16676) covalent geometry : angle 0.57191 / 0.29 (22616) hydrogen bonds : bond 0.03908 / 2.63 ( 752) hydrogen bonds : angle 4.54451 / 3.34 ( 1992) Misc. bond : bond 0.00524 / 0.25 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4655 (ttt) REVERT: A 180 HIS cc_start: 0.7633 (t-90) cc_final: 0.7216 (m-70) REVERT: A 315 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7581 (p90) REVERT: A 346 GLU cc_start: 0.7724 (pm20) cc_final: 0.7309 (pm20) REVERT: A 491 VAL cc_start: 0.5818 (OUTLIER) cc_final: 0.5510 (m) REVERT: A 496 GLU cc_start: 0.7805 (tp30) cc_final: 0.7349 (pp20) REVERT: B 115 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.4700 (ttt) REVERT: B 180 HIS cc_start: 0.7608 (t-90) cc_final: 0.7201 (m-70) REVERT: B 315 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7574 (p90) REVERT: B 344 ASP cc_start: 0.6741 (t0) cc_final: 0.6410 (t0) REVERT: B 346 GLU cc_start: 0.7699 (pm20) cc_final: 0.7282 (pm20) REVERT: B 491 VAL cc_start: 0.5846 (OUTLIER) cc_final: 0.5550 (m) REVERT: B 496 GLU cc_start: 0.7810 (tp30) cc_final: 0.7355 (pp20) REVERT: B 549 LEU cc_start: 0.7437 (pp) cc_final: 0.7219 (pt) REVERT: C 115 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4678 (ttt) REVERT: C 180 HIS cc_start: 0.7606 (t-90) cc_final: 0.7196 (m-70) REVERT: C 315 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7602 (p90) REVERT: C 326 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7287 (mp10) REVERT: C 346 GLU cc_start: 0.7705 (pm20) cc_final: 0.7300 (pm20) REVERT: C 496 GLU cc_start: 0.7903 (tp30) cc_final: 0.7286 (pp20) REVERT: C 549 LEU cc_start: 0.7484 (pp) cc_final: 0.7224 (pt) REVERT: D 115 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.4705 (ttt) REVERT: D 180 HIS cc_start: 0.7607 (t-90) cc_final: 0.7205 (m-70) REVERT: D 315 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7598 (p90) REVERT: D 326 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7278 (mp10) REVERT: D 344 ASP cc_start: 0.6745 (t0) cc_final: 0.6419 (t0) REVERT: D 346 GLU cc_start: 0.7691 (pm20) cc_final: 0.7282 (pm20) REVERT: D 496 GLU cc_start: 0.7920 (tp30) cc_final: 0.7296 (pp20) REVERT: D 549 LEU cc_start: 0.7475 (pp) cc_final: 0.7222 (pt) outliers start: 19 outliers final: 5 residues processed: 171 average time/residue: 0.8433 time to fit residues: 155.4675 Evaluate side-chains 163 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 9.9990 chunk 28 optimal weight: 0.1980 chunk 163 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135152 restraints weight = 16034.064| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.74 r_work: 0.3575 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16684 Z= 0.165 Angle : 0.630 12.410 22616 Z= 0.320 Chirality : 0.046 0.164 2388 Planarity : 0.014 0.346 2884 Dihedral : 9.631 90.019 2588 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.21 % Allowed : 16.05 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.19), residues: 1940 helix: 0.76 (0.17), residues: 896 sheet: -0.37 (0.45), residues: 148 loop : -0.49 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG A 451 TYR 0.050 0.002 TYR B 456 PHE 0.015 0.002 PHE C 363 TRP 0.011 0.001 TRP C 285 HIS 0.007 0.002 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (16676) covalent geometry : angle 0.62972 / 0.32 (22616) hydrogen bonds : bond 0.04696 / 3.17 ( 752) hydrogen bonds : angle 4.74490 / 3.50 ( 1992) Misc. bond : bond 0.00655 / 0.31 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7628.49 seconds wall clock time: 130 minutes 25.61 seconds (7825.61 seconds total)