Starting phenix.real_space_refine on Wed Mar 4 16:33:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etp_28595/03_2026/8etp_28595.map" } resolution = 3.52 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= 0.003 sd= 0.077 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 4 5.49 5 S 66 5.16 5 C 9652 2.51 5 N 2410 2.21 5 O 2677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14809 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Conformer: "B" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} bond proxies already assigned to first conformer: 3758 Chain: "B" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.86, per 1000 atoms: 0.26 Number of scatterers: 14809 At special positions: 0 Unit cell: (132.25, 118.496, 106.858, 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 66 16.00 P 4 15.00 O 2677 8.00 N 2410 7.00 C 9652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 587.2 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 67.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 165 through 193 removed outlier: 3.917A pdb=" N TYR A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.766A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.662A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.065A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.840A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.958A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.232A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 removed outlier: 3.644A pdb=" N THR A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 609 Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.816A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.901A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.971A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 270 through 280 removed outlier: 3.885A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 280 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 427 removed outlier: 5.280A pdb=" N SER B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG B 410 " --> pdb=" O MET B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.979A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 6.240A pdb=" N ILE B 482 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 484 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.743A pdb=" N TYR C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 4.008A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.774A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.553A pdb=" N PHE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 279 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.532A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 427 removed outlier: 5.701A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 461 through 478 removed outlier: 6.114A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'D' and resid 215 through 242 removed outlier: 3.658A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.633A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 3.920A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.625A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 3.633A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 320 through 329 removed outlier: 3.502A pdb=" N PHE D 323 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 328 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.298A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.313A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.856A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.595A pdb=" N SER D 594 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 595 " --> pdb=" O GLU D 592 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU D 596 " --> pdb=" O ILE D 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 596' Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.745A pdb=" N LEU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.768A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.694A pdb=" N TYR A 508 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER A 570 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 528 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 removed outlier: 3.642A pdb=" N GLU B 228 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.558A pdb=" N ILE B 521 " --> pdb=" O PHE B 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 7.161A pdb=" N ILE B 568 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 527 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL B 540 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 529 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 7.060A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 527 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL C 540 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C 529 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.789A pdb=" N ARG D 279 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 542 removed outlier: 3.511A pdb=" N ASN D 615 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 7.241A pdb=" N VAL D 608 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 607 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 571 " --> pdb=" O VAL D 582 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2690 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: 2.25 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2339 1.31 - 1.44: 4238 1.44 - 1.56: 8474 1.56 - 1.69: 10 1.69 - 1.82: 105 Bond restraints: 15166 Sorted by residual: bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.617 1.512 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 15161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 20392 3.67 - 7.35: 134 7.35 - 11.02: 52 11.02 - 14.70: 7 14.70 - 18.37: 9 Bond angle restraints: 20594 Sorted by residual: angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.22 -18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.05 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 127.89 -18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 127.84 -17.99 3.00e+00 1.11e-01 3.60e+01 angle pdb=" O1A PCG A 802 " pdb=" PA PCG A 802 " pdb=" O5' PCG A 802 " ideal model delta sigma weight residual 102.28 117.95 -15.67 3.00e+00 1.11e-01 2.73e+01 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.76: 8758 31.76 - 63.51: 293 63.51 - 95.27: 26 95.27 - 127.03: 3 127.03 - 158.78: 3 Dihedral angle restraints: 9083 sinusoidal: 3774 harmonic: 5309 Sorted by residual: dihedral pdb=" C ALA A 566 " pdb=" N ALA A 566 " pdb=" CA ALA A 566 " pdb=" CB ALA A 566 " ideal model delta harmonic sigma weight residual -122.60 -134.31 11.71 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" N ALA A 566 " pdb=" C ALA A 566 " pdb=" CA ALA A 566 " pdb=" CB ALA A 566 " ideal model delta harmonic sigma weight residual 122.90 134.59 -11.69 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" C5' PCG C 802 " pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " pdb=" O2A PCG C 802 " ideal model delta sinusoidal sigma weight residual 81.13 -77.65 158.78 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 9080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 2338 0.353 - 0.706: 1 0.706 - 1.058: 0 1.058 - 1.411: 0 1.411 - 1.764: 4 Chirality restraints: 2343 Sorted by residual: chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.73 -1.76 2.00e-01 2.50e+01 7.78e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.50 -0.74 -1.76 2.00e-01 2.50e+01 7.74e+01 chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.81 -1.68 2.00e-01 2.50e+01 7.09e+01 ... (remaining 2340 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 562 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ASN A 562 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 562 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 563 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.73e+00 pdb=" N PRO D 273 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 504 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO C 505 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 505 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 505 " -0.038 5.00e-02 4.00e+02 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4934 2.85 - 3.36: 13261 3.36 - 3.87: 25023 3.87 - 4.39: 27322 4.39 - 4.90: 47477 Nonbonded interactions: 118017 Sorted by model distance: nonbonded pdb=" OG SER C 504 " pdb=" OD1 ASP C 507 " model vdw 2.332 3.040 nonbonded pdb=" O PHE D 516 " pdb=" OG SER D 520 " model vdw 2.339 3.040 nonbonded pdb=" O ALA B 415 " pdb=" OG SER B 419 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" OD1 ASP A 432 " model vdw 2.370 3.040 nonbonded pdb=" OE1 GLU D 560 " pdb=" OH TYR D 562 " model vdw 2.371 3.040 ... (remaining 118012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 391 or resid 393 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 802)) selection = (chain 'C' and (resid 159 through 391 or resid 393 through 610 or resid 801 thro \ ugh 802)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.580 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.250 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.006 0.117 15169 Z= 0.309 Angle : 1.012 18.372 20603 Z= 0.509 Chirality : 0.090 1.764 2343 Planarity : 0.007 0.074 2533 Dihedral : 16.202 158.782 5675 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Cbeta Deviations : 0.12 % 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: -3.88 (0.14), residues: 1792 helix: -2.65 (0.09), residues: 1166 sheet: -2.64 (0.57), residues: 63 loop : -1.87 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 603 TYR 0.026 0.002 TYR C 184 PHE 0.024 0.002 PHE C 180 TRP 0.015 0.002 TRP A 203 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00599 (15166) covalent geometry : angle 1.01137 (20594) hydrogen bonds : bond 0.10687 ( 920) hydrogen bonds : angle 5.77819 ( 2690) link_NAG-ASN : bond 0.00174 ( 3) link_NAG-ASN : angle 2.10437 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7376 (pt0) REVERT: A 228 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 241 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7444 (mm-40) REVERT: A 271 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8349 (Cg_exo) REVERT: A 581 LYS cc_start: 0.8792 (tttm) cc_final: 0.8503 (tptt) REVERT: B 263 TYR cc_start: 0.7835 (m-10) cc_final: 0.7578 (m-80) REVERT: B 271 PRO cc_start: 0.7872 (Cg_endo) cc_final: 0.7617 (Cg_exo) REVERT: B 305 ASN cc_start: 0.8387 (t0) cc_final: 0.8184 (t0) REVERT: B 422 GLN cc_start: 0.8427 (tt0) cc_final: 0.8002 (tt0) REVERT: B 524 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6687 (tm-30) REVERT: B 551 SER cc_start: 0.7782 (p) cc_final: 0.7477 (t) REVERT: C 240 TRP cc_start: 0.8072 (t-100) cc_final: 0.7557 (t60) REVERT: C 311 LEU cc_start: 0.8326 (mt) cc_final: 0.7733 (tt) REVERT: C 439 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7501 (ttt90) REVERT: C 497 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8779 (mmmm) REVERT: C 607 MET cc_start: 0.6645 (mtp) cc_final: 0.6286 (mtm) REVERT: D 267 ASP cc_start: 0.8362 (t70) cc_final: 0.7492 (t0) REVERT: D 441 MET cc_start: 0.8447 (mmt) cc_final: 0.8066 (mmt) REVERT: D 466 MET cc_start: 0.8371 (mtm) cc_final: 0.8109 (mtm) REVERT: D 500 LYS cc_start: 0.8513 (pttp) cc_final: 0.8313 (pttm) REVERT: D 534 TYR cc_start: 0.8043 (m-10) cc_final: 0.7794 (m-10) REVERT: D 641 LYS cc_start: 0.7271 (mttt) cc_final: 0.6894 (tppt) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1259 time to fit residues: 58.2626 Evaluate side-chains 215 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 562 ASN A 567 ASN B 196 GLN B 276 ASN B 317 ASN B 471 ASN C 237 ASN C 407 ASN C 425 GLN D 365 HIS D 423 GLN D 440 GLN D 607 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124606 restraints weight = 28229.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125192 restraints weight = 20076.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126640 restraints weight = 16802.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127417 restraints weight = 11514.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127987 restraints weight = 10929.757| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15169 Z= 0.121 Angle : 0.523 8.081 20603 Z= 0.277 Chirality : 0.040 0.154 2343 Planarity : 0.005 0.054 2533 Dihedral : 10.597 178.743 2180 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.61 % Allowed : 12.21 % Favored : 86.18 % 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: -0.82 (0.18), residues: 1792 helix: -0.06 (0.14), residues: 1168 sheet: -1.40 (0.65), residues: 55 loop : -1.24 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 636 TYR 0.014 0.001 TYR C 357 PHE 0.013 0.001 PHE D 516 TRP 0.014 0.001 TRP D 231 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00262 (15166) covalent geometry : angle 0.52078 (20594) hydrogen bonds : bond 0.03806 ( 920) hydrogen bonds : angle 4.13267 ( 2690) link_NAG-ASN : bond 0.00099 ( 3) link_NAG-ASN : angle 2.19919 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 240 TRP cc_start: 0.8357 (t-100) cc_final: 0.7641 (t60) REVERT: A 241 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7561 (mm110) REVERT: A 352 TYR cc_start: 0.8806 (t80) cc_final: 0.8573 (t80) REVERT: A 395 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7144 (mt) REVERT: A 422 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 465 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7418 (mtmm) REVERT: A 581 LYS cc_start: 0.8587 (tttm) cc_final: 0.8297 (tptt) REVERT: A 583 ASP cc_start: 0.6352 (m-30) cc_final: 0.6077 (m-30) REVERT: B 422 GLN cc_start: 0.8339 (tt0) cc_final: 0.7830 (mt0) REVERT: B 524 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6886 (tm-30) REVERT: B 551 SER cc_start: 0.8155 (p) cc_final: 0.7841 (t) REVERT: B 575 ASP cc_start: 0.7461 (t0) cc_final: 0.7062 (t0) REVERT: C 311 LEU cc_start: 0.8254 (mt) cc_final: 0.7872 (tt) REVERT: C 376 GLU cc_start: 0.8280 (pm20) cc_final: 0.7735 (tt0) REVERT: C 422 GLN cc_start: 0.8520 (tp40) cc_final: 0.8284 (tp-100) REVERT: C 439 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7532 (ttt90) REVERT: C 481 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7340 (ptm160) REVERT: C 604 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8142 (mm-40) REVERT: D 267 ASP cc_start: 0.8112 (t70) cc_final: 0.7222 (t0) REVERT: D 268 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7969 (mtm) outliers start: 26 outliers final: 11 residues processed: 259 average time/residue: 0.1119 time to fit residues: 44.2835 Evaluate side-chains 220 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 0.0270 chunk 121 optimal weight: 1.9990 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 305 ASN C 425 GLN C 484 GLN D 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124234 restraints weight = 23489.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124763 restraints weight = 18904.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126366 restraints weight = 16802.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127020 restraints weight = 11434.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127168 restraints weight = 11046.229| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15169 Z= 0.109 Angle : 0.484 8.161 20603 Z= 0.257 Chirality : 0.040 0.149 2343 Planarity : 0.004 0.051 2533 Dihedral : 10.215 177.955 2180 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.73 % Allowed : 14.62 % Favored : 83.64 % 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: 0.51 (0.20), residues: 1792 helix: 1.02 (0.15), residues: 1167 sheet: -0.87 (0.64), residues: 51 loop : -0.87 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 636 TYR 0.013 0.001 TYR C 357 PHE 0.012 0.001 PHE D 270 TRP 0.027 0.001 TRP B 316 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00235 (15166) covalent geometry : angle 0.48224 (20594) hydrogen bonds : bond 0.03605 ( 920) hydrogen bonds : angle 3.81547 ( 2690) link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 2.15816 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 240 TRP cc_start: 0.8260 (t-100) cc_final: 0.7670 (t60) REVERT: A 241 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7512 (mm110) REVERT: A 352 TYR cc_start: 0.8611 (t80) cc_final: 0.8368 (t80) REVERT: A 395 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7112 (mt) REVERT: A 422 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 482 ILE cc_start: 0.8027 (pt) cc_final: 0.7663 (mt) REVERT: B 418 ASP cc_start: 0.7291 (t70) cc_final: 0.7017 (t0) REVERT: B 422 GLN cc_start: 0.8099 (tt0) cc_final: 0.7699 (mt0) REVERT: B 551 SER cc_start: 0.7957 (p) cc_final: 0.7650 (t) REVERT: B 575 ASP cc_start: 0.7538 (t0) cc_final: 0.7104 (t0) REVERT: C 241 GLN cc_start: 0.7977 (mp10) cc_final: 0.7402 (mp10) REVERT: C 311 LEU cc_start: 0.8278 (mt) cc_final: 0.7988 (tt) REVERT: C 439 ARG cc_start: 0.7800 (ttt90) cc_final: 0.7517 (ttt90) REVERT: D 267 ASP cc_start: 0.7941 (t70) cc_final: 0.7119 (t0) outliers start: 28 outliers final: 15 residues processed: 239 average time/residue: 0.1042 time to fit residues: 38.2896 Evaluate side-chains 225 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 4 optimal weight: 0.0020 chunk 168 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN C 299 ASN C 422 GLN C 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123775 restraints weight = 23288.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125038 restraints weight = 19434.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126016 restraints weight = 15384.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126681 restraints weight = 12245.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126817 restraints weight = 11632.406| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15169 Z= 0.106 Angle : 0.486 7.842 20603 Z= 0.256 Chirality : 0.040 0.150 2343 Planarity : 0.004 0.049 2533 Dihedral : 10.024 178.026 2180 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.67 % Allowed : 15.61 % Favored : 82.71 % 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: 1.13 (0.20), residues: 1792 helix: 1.50 (0.15), residues: 1163 sheet: -0.62 (0.69), residues: 46 loop : -0.60 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 603 TYR 0.013 0.001 TYR C 357 PHE 0.011 0.001 PHE B 547 TRP 0.040 0.001 TRP B 316 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00229 (15166) covalent geometry : angle 0.48409 (20594) hydrogen bonds : bond 0.03517 ( 920) hydrogen bonds : angle 3.69848 ( 2690) link_NAG-ASN : bond 0.00042 ( 3) link_NAG-ASN : angle 2.18011 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 240 TRP cc_start: 0.8280 (t-100) cc_final: 0.7683 (t60) REVERT: A 241 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7488 (mm110) REVERT: A 395 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7020 (mt) REVERT: A 405 ASN cc_start: 0.7795 (t0) cc_final: 0.7329 (t0) REVERT: A 482 ILE cc_start: 0.8026 (pt) cc_final: 0.7604 (mt) REVERT: B 316 TRP cc_start: 0.8540 (m100) cc_final: 0.8336 (m100) REVERT: B 418 ASP cc_start: 0.7204 (t70) cc_final: 0.6983 (t0) REVERT: B 422 GLN cc_start: 0.8049 (tt0) cc_final: 0.7675 (mt0) REVERT: B 551 SER cc_start: 0.7895 (p) cc_final: 0.7539 (t) REVERT: B 575 ASP cc_start: 0.7534 (t0) cc_final: 0.7200 (t0) REVERT: C 241 GLN cc_start: 0.7964 (mp10) cc_final: 0.7429 (mp10) REVERT: C 311 LEU cc_start: 0.8231 (mt) cc_final: 0.7982 (tt) REVERT: C 439 ARG cc_start: 0.7769 (ttt90) cc_final: 0.7490 (ttt90) REVERT: D 267 ASP cc_start: 0.7848 (t70) cc_final: 0.6956 (t0) REVERT: D 268 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7865 (mtm) REVERT: D 339 HIS cc_start: 0.6956 (t-90) cc_final: 0.6714 (t-90) REVERT: D 536 MET cc_start: 0.8399 (ttm) cc_final: 0.8183 (ttp) outliers start: 27 outliers final: 15 residues processed: 237 average time/residue: 0.0997 time to fit residues: 36.6127 Evaluate side-chains 218 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 147 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 167 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN C 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123455 restraints weight = 29912.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123695 restraints weight = 22785.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125129 restraints weight = 18692.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125711 restraints weight = 12827.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126415 restraints weight = 12281.641| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15169 Z= 0.120 Angle : 0.495 8.054 20603 Z= 0.260 Chirality : 0.040 0.160 2343 Planarity : 0.004 0.047 2533 Dihedral : 9.914 177.699 2180 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.86 % Allowed : 16.23 % Favored : 81.91 % 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: 1.31 (0.21), residues: 1792 helix: 1.64 (0.15), residues: 1167 sheet: -0.53 (0.70), residues: 46 loop : -0.56 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 239 TYR 0.014 0.001 TYR C 357 PHE 0.011 0.001 PHE C 301 TRP 0.026 0.001 TRP B 316 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00269 (15166) covalent geometry : angle 0.49288 (20594) hydrogen bonds : bond 0.03572 ( 920) hydrogen bonds : angle 3.67950 ( 2690) link_NAG-ASN : bond 0.00043 ( 3) link_NAG-ASN : angle 2.15017 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 241 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7509 (mm110) REVERT: A 395 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7120 (mt) REVERT: A 422 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 418 ASP cc_start: 0.7391 (t70) cc_final: 0.7099 (t0) REVERT: B 422 GLN cc_start: 0.8141 (tt0) cc_final: 0.7790 (mt0) REVERT: B 575 ASP cc_start: 0.7499 (t0) cc_final: 0.7148 (t0) REVERT: C 241 GLN cc_start: 0.8013 (mp10) cc_final: 0.7550 (mp10) REVERT: C 311 LEU cc_start: 0.8269 (mt) cc_final: 0.7940 (tt) REVERT: C 376 GLU cc_start: 0.6063 (tt0) cc_final: 0.5767 (tt0) REVERT: C 439 ARG cc_start: 0.7852 (ttt90) cc_final: 0.7549 (ttt90) REVERT: D 267 ASP cc_start: 0.7956 (t70) cc_final: 0.7069 (t0) REVERT: D 268 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: D 339 HIS cc_start: 0.7128 (t-90) cc_final: 0.6870 (t-90) REVERT: D 536 MET cc_start: 0.8576 (ttm) cc_final: 0.8326 (ttp) outliers start: 30 outliers final: 20 residues processed: 226 average time/residue: 0.0995 time to fit residues: 35.6511 Evaluate side-chains 220 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN C 422 GLN C 425 GLN C 447 ASN D 453 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120832 restraints weight = 23212.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122751 restraints weight = 17234.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123593 restraints weight = 13943.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124187 restraints weight = 10882.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124346 restraints weight = 10003.330| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15169 Z= 0.126 Angle : 0.499 8.244 20603 Z= 0.262 Chirality : 0.040 0.156 2343 Planarity : 0.004 0.048 2533 Dihedral : 9.813 177.327 2180 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.98 % Allowed : 17.16 % Favored : 80.86 % 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: 1.44 (0.21), residues: 1792 helix: 1.74 (0.15), residues: 1167 sheet: -0.56 (0.70), residues: 46 loop : -0.50 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.014 0.001 TYR D 351 PHE 0.012 0.001 PHE C 301 TRP 0.050 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00286 (15166) covalent geometry : angle 0.49750 (20594) hydrogen bonds : bond 0.03606 ( 920) hydrogen bonds : angle 3.66399 ( 2690) link_NAG-ASN : bond 0.00046 ( 3) link_NAG-ASN : angle 2.09512 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 241 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7523 (mm110) REVERT: A 395 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7103 (mt) REVERT: A 422 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 305 ASN cc_start: 0.8403 (t0) cc_final: 0.8167 (t0) REVERT: B 418 ASP cc_start: 0.7392 (t70) cc_final: 0.7103 (t0) REVERT: B 422 GLN cc_start: 0.8177 (tt0) cc_final: 0.7806 (mt0) REVERT: B 519 MET cc_start: 0.7438 (tpp) cc_final: 0.7208 (tpt) REVERT: B 575 ASP cc_start: 0.7625 (t0) cc_final: 0.7269 (t0) REVERT: C 241 GLN cc_start: 0.7970 (mp10) cc_final: 0.7507 (mp10) REVERT: C 439 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7537 (ttt90) REVERT: C 480 VAL cc_start: 0.8798 (t) cc_final: 0.8174 (t) REVERT: D 267 ASP cc_start: 0.7996 (t70) cc_final: 0.7124 (t0) REVERT: D 536 MET cc_start: 0.8588 (ttm) cc_final: 0.8343 (ttp) outliers start: 32 outliers final: 22 residues processed: 225 average time/residue: 0.0965 time to fit residues: 34.3230 Evaluate side-chains 220 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 23 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN C 425 GLN C 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121608 restraints weight = 23376.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122390 restraints weight = 18050.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123269 restraints weight = 16453.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123891 restraints weight = 12689.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124148 restraints weight = 11929.931| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15169 Z= 0.125 Angle : 0.505 8.071 20603 Z= 0.267 Chirality : 0.040 0.181 2343 Planarity : 0.004 0.050 2533 Dihedral : 9.735 177.901 2180 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.80 % Allowed : 17.84 % Favored : 80.36 % 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: 1.55 (0.21), residues: 1792 helix: 1.81 (0.15), residues: 1167 sheet: -0.56 (0.70), residues: 46 loop : -0.41 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.014 0.001 TYR D 351 PHE 0.012 0.001 PHE C 483 TRP 0.061 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00283 (15166) covalent geometry : angle 0.50369 (20594) hydrogen bonds : bond 0.03596 ( 920) hydrogen bonds : angle 3.65391 ( 2690) link_NAG-ASN : bond 0.00034 ( 3) link_NAG-ASN : angle 2.06742 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 241 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7501 (mm110) REVERT: A 395 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7182 (mt) REVERT: A 422 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 305 ASN cc_start: 0.8393 (t0) cc_final: 0.8163 (t0) REVERT: B 418 ASP cc_start: 0.7217 (t70) cc_final: 0.6947 (t0) REVERT: B 422 GLN cc_start: 0.8017 (tt0) cc_final: 0.7662 (mt0) REVERT: B 575 ASP cc_start: 0.7509 (t0) cc_final: 0.7211 (t0) REVERT: C 439 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7531 (ttt90) REVERT: D 267 ASP cc_start: 0.7823 (t70) cc_final: 0.6990 (t0) REVERT: D 536 MET cc_start: 0.8450 (ttm) cc_final: 0.8220 (ttp) outliers start: 29 outliers final: 21 residues processed: 225 average time/residue: 0.0938 time to fit residues: 33.5507 Evaluate side-chains 223 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 122 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN B 523 ASN C 229 GLN C 422 GLN C 425 GLN C 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121305 restraints weight = 23789.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123117 restraints weight = 17771.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124088 restraints weight = 14738.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124562 restraints weight = 11184.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124742 restraints weight = 10240.111| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15169 Z= 0.118 Angle : 0.516 9.469 20603 Z= 0.269 Chirality : 0.040 0.200 2343 Planarity : 0.004 0.051 2533 Dihedral : 9.638 178.765 2180 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.55 % Allowed : 18.46 % Favored : 79.99 % 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: 1.72 (0.21), residues: 1792 helix: 1.94 (0.15), residues: 1153 sheet: -0.59 (0.70), residues: 46 loop : -0.27 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.013 0.001 TYR C 357 PHE 0.013 0.001 PHE C 180 TRP 0.047 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00265 (15166) covalent geometry : angle 0.51412 (20594) hydrogen bonds : bond 0.03548 ( 920) hydrogen bonds : angle 3.63301 ( 2690) link_NAG-ASN : bond 0.00021 ( 3) link_NAG-ASN : angle 2.07621 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 395 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7051 (mt) REVERT: A 422 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 305 ASN cc_start: 0.8423 (t0) cc_final: 0.8158 (t0) REVERT: B 316 TRP cc_start: 0.8537 (m100) cc_final: 0.8195 (m100) REVERT: B 418 ASP cc_start: 0.7505 (t70) cc_final: 0.7217 (t0) REVERT: B 422 GLN cc_start: 0.8194 (tt0) cc_final: 0.7832 (mt0) REVERT: B 575 ASP cc_start: 0.7655 (t0) cc_final: 0.7346 (t0) REVERT: C 241 GLN cc_start: 0.7955 (mp10) cc_final: 0.7429 (mp10) REVERT: C 439 ARG cc_start: 0.7966 (ttt90) cc_final: 0.7568 (ttt90) REVERT: D 267 ASP cc_start: 0.8000 (t70) cc_final: 0.7124 (t0) REVERT: D 339 HIS cc_start: 0.7144 (t-90) cc_final: 0.6842 (t-90) REVERT: D 536 MET cc_start: 0.8632 (ttm) cc_final: 0.8338 (ttp) outliers start: 25 outliers final: 20 residues processed: 226 average time/residue: 0.1015 time to fit residues: 36.1863 Evaluate side-chains 219 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 177 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 422 GLN C 229 GLN C 422 GLN C 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121417 restraints weight = 23463.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123398 restraints weight = 17721.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124371 restraints weight = 14021.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125211 restraints weight = 11027.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125308 restraints weight = 10120.743| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15169 Z= 0.119 Angle : 0.519 8.564 20603 Z= 0.270 Chirality : 0.040 0.205 2343 Planarity : 0.004 0.051 2533 Dihedral : 9.580 179.221 2180 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.49 % Allowed : 18.84 % Favored : 79.68 % 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: 1.75 (0.21), residues: 1792 helix: 1.97 (0.15), residues: 1153 sheet: -0.64 (0.70), residues: 46 loop : -0.26 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.025 0.001 TYR D 229 PHE 0.011 0.001 PHE B 547 TRP 0.048 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00266 (15166) covalent geometry : angle 0.51773 (20594) hydrogen bonds : bond 0.03543 ( 920) hydrogen bonds : angle 3.63153 ( 2690) link_NAG-ASN : bond 0.00024 ( 3) link_NAG-ASN : angle 2.07799 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 395 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7071 (mt) REVERT: A 422 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7483 (tm-30) REVERT: B 305 ASN cc_start: 0.8430 (t0) cc_final: 0.8165 (t0) REVERT: B 418 ASP cc_start: 0.7529 (t70) cc_final: 0.7229 (t0) REVERT: B 422 GLN cc_start: 0.8182 (tt0) cc_final: 0.7873 (mt0) REVERT: B 575 ASP cc_start: 0.7746 (t0) cc_final: 0.7521 (t0) REVERT: C 241 GLN cc_start: 0.7968 (mp10) cc_final: 0.7447 (mp10) REVERT: C 439 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7546 (ttt90) REVERT: D 536 MET cc_start: 0.8556 (ttm) cc_final: 0.8310 (ttp) outliers start: 24 outliers final: 22 residues processed: 222 average time/residue: 0.0966 time to fit residues: 34.0324 Evaluate side-chains 219 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 16 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125194 restraints weight = 23424.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126091 restraints weight = 16707.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127425 restraints weight = 14613.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127991 restraints weight = 11268.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128450 restraints weight = 10810.289| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15169 Z= 0.118 Angle : 0.544 11.107 20603 Z= 0.277 Chirality : 0.041 0.206 2343 Planarity : 0.004 0.052 2533 Dihedral : 9.561 179.613 2180 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 19.58 % Favored : 78.93 % 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: 1.79 (0.21), residues: 1792 helix: 2.00 (0.15), residues: 1153 sheet: -0.64 (0.71), residues: 46 loop : -0.24 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 499 TYR 0.037 0.001 TYR D 229 PHE 0.011 0.001 PHE B 547 TRP 0.070 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00265 (15166) covalent geometry : angle 0.54243 (20594) hydrogen bonds : bond 0.03531 ( 920) hydrogen bonds : angle 3.61793 ( 2690) link_NAG-ASN : bond 0.00007 ( 3) link_NAG-ASN : angle 2.04517 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 395 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7069 (mt) REVERT: B 418 ASP cc_start: 0.7299 (t70) cc_final: 0.7020 (t0) REVERT: B 422 GLN cc_start: 0.8010 (tt0) cc_final: 0.7711 (mt0) REVERT: C 241 GLN cc_start: 0.7907 (mp10) cc_final: 0.7455 (mp10) REVERT: C 439 ARG cc_start: 0.7894 (ttt90) cc_final: 0.7514 (ttt90) REVERT: D 536 MET cc_start: 0.8399 (ttm) cc_final: 0.8169 (ttp) outliers start: 24 outliers final: 21 residues processed: 213 average time/residue: 0.1014 time to fit residues: 33.9119 Evaluate side-chains 217 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 159 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 145 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126375 restraints weight = 20929.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128489 restraints weight = 14434.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129821 restraints weight = 10359.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130320 restraints weight = 8059.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130428 restraints weight = 7531.726| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15169 Z= 0.106 Angle : 0.526 10.934 20603 Z= 0.270 Chirality : 0.040 0.209 2343 Planarity : 0.004 0.052 2533 Dihedral : 9.501 179.548 2180 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.30 % Allowed : 20.14 % Favored : 78.56 % 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: 1.87 (0.21), residues: 1792 helix: 2.04 (0.15), residues: 1152 sheet: -0.52 (0.72), residues: 46 loop : -0.16 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 499 TYR 0.035 0.001 TYR D 229 PHE 0.012 0.001 PHE B 547 TRP 0.051 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00227 (15166) covalent geometry : angle 0.52486 (20594) hydrogen bonds : bond 0.03382 ( 920) hydrogen bonds : angle 3.56335 ( 2690) link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 1.96094 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.16 seconds wall clock time: 41 minutes 8.10 seconds (2468.10 seconds total)