Starting phenix.real_space_refine on Mon Aug 25 22:02:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn2_19384/08_2025/8rn2_19384.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 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 S 116 5.16 5 C 9845 2.51 5 N 2639 2.21 5 O 2904 1.98 5 H 15574 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31078 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 11326 Classifications: {'peptide': 706} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 679} Chain breaks: 1 Chain: "B" Number of atoms: 9951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 9951 Classifications: {'peptide': 635} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 601} Chain breaks: 2 Chain: "C" Number of atoms: 9801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9801 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 1 Time building chain proxies: 4.67, per 1000 atoms: 0.15 Number of scatterers: 31078 At special positions: 0 Unit cell: (126, 109.2, 134.4, 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 116 16.00 O 2904 8.00 N 2639 7.00 C 9845 6.00 H 15574 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 813.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3622 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 23 sheets defined 48.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 25 removed outlier: 4.041A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 52 removed outlier: 3.985A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.747A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.943A pdb=" N VAL A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.632A pdb=" N SER A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.552A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.549A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.644A pdb=" N TYR A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.521A pdb=" N ARG A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 358 through 366 removed outlier: 4.383A pdb=" N ALA A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.084A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.570A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 575 through 595 removed outlier: 3.729A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 671 removed outlier: 3.624A pdb=" N ARG A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 716 removed outlier: 3.700A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.997A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.748A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.855A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.514A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.583A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.697A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.650A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 473 Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.766A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.106A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.539A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.232A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.910A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.570A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.826A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 534 through 541 removed outlier: 4.373A pdb=" N GLU C 539 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 Processing helix chain 'C' and resid 557 through 566 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.880A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 606 removed outlier: 4.532A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 3.719A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 689 through 694 removed outlier: 4.124A pdb=" N ASN C 692 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 693 " --> pdb=" O MET C 690 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 694' Processing helix chain 'C' and resid 713 through 720 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.591A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.047A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.538A pdb=" N LEU A 496 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.538A pdb=" N LEU A 496 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 492 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN A 487 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 477 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.565A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 628 removed outlier: 5.912A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 188 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 244 removed outlier: 6.773A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.285A pdb=" N GLN C 91 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.994A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.714A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 480 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU C 386 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 342 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 499 removed outlier: 3.942A pdb=" N MET C 514 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC4, first strand: chain 'C' and resid 660 through 662 removed outlier: 3.919A pdb=" N VAL C 667 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 698 through 700 removed outlier: 3.584A pdb=" N VAL C 738 " --> pdb=" O ALA C 726 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 2058 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: 7.34 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15538 1.03 - 1.23: 54 1.23 - 1.42: 6447 1.42 - 1.62: 9145 1.62 - 1.82: 196 Bond restraints: 31380 Sorted by residual: bond pdb=" CA SER C 256 " pdb=" CB SER C 256 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" N ASP C 705 " pdb=" CA ASP C 705 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.13e-02 7.83e+03 9.34e+00 bond pdb=" N VAL B 273 " pdb=" CA VAL B 273 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.35e+00 bond pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.01e-02 9.80e+03 7.68e+00 bond pdb=" N THR C 254 " pdb=" H THR C 254 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.55e+00 ... (remaining 31375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 55950 1.58 - 3.16: 752 3.16 - 4.74: 97 4.74 - 6.32: 8 6.32 - 7.90: 4 Bond angle restraints: 56811 Sorted by residual: angle pdb=" CA LEU B 271 " pdb=" C LEU B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 117.67 124.11 -6.44 1.08e+00 8.57e-01 3.56e+01 angle pdb=" O LEU B 271 " pdb=" C LEU B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 121.55 117.41 4.14 7.80e-01 1.64e+00 2.81e+01 angle pdb=" N SER B 269 " pdb=" CA SER B 269 " pdb=" C SER B 269 " ideal model delta sigma weight residual 110.64 103.24 7.40 1.48e+00 4.57e-01 2.50e+01 angle pdb=" CA SER B 269 " pdb=" C SER B 269 " pdb=" O SER B 269 " ideal model delta sigma weight residual 120.88 116.47 4.41 9.40e-01 1.13e+00 2.21e+01 angle pdb=" CA THR C 254 " pdb=" C THR C 254 " pdb=" O THR C 254 " ideal model delta sigma weight residual 120.90 116.15 4.75 1.07e+00 8.73e-01 1.97e+01 ... (remaining 56806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12828 17.93 - 35.86: 1250 35.86 - 53.78: 462 53.78 - 71.71: 119 71.71 - 89.64: 20 Dihedral angle restraints: 14679 sinusoidal: 8124 harmonic: 6555 Sorted by residual: dihedral pdb=" CA MET C 610 " pdb=" C MET C 610 " pdb=" N LYS C 611 " pdb=" CA LYS C 611 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG B 601 " pdb=" CD ARG B 601 " pdb=" NE ARG B 601 " pdb=" CZ ARG B 601 " ideal model delta sinusoidal sigma weight residual -90.00 -39.99 -50.01 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP C 343 " pdb=" CB ASP C 343 " pdb=" CG ASP C 343 " pdb=" OD1 ASP C 343 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1934 0.046 - 0.091: 296 0.091 - 0.137: 96 0.137 - 0.183: 3 0.183 - 0.229: 4 Chirality restraints: 2333 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LYS C 252 " pdb=" N LYS C 252 " pdb=" C LYS C 252 " pdb=" CB LYS C 252 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2330 not shown) Planarity restraints: 4602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 251 " 0.056 2.00e-02 2.50e+03 5.96e-02 5.33e+01 pdb=" CG ASN C 251 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 251 " -0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 251 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 251 " -0.087 2.00e-02 2.50e+03 pdb="HD22 ASN C 251 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 270 " -0.027 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" N LEU B 271 " 0.084 2.00e-02 2.50e+03 pdb=" CA LEU B 271 " -0.021 2.00e-02 2.50e+03 pdb=" H LEU B 271 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 484 " -0.225 9.50e-02 1.11e+02 7.53e-02 6.96e+00 pdb=" NE ARG A 484 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 484 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 484 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 484 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 484 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 484 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 484 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 484 " -0.001 2.00e-02 2.50e+03 ... (remaining 4599 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1006 2.13 - 2.75: 58416 2.75 - 3.37: 89846 3.37 - 3.98: 116157 3.98 - 4.60: 183778 Nonbonded interactions: 449203 Sorted by model distance: nonbonded pdb=" O GLN A 566 " pdb="HE21 GLN A 566 " model vdw 1.518 2.450 nonbonded pdb=" HG2 LYS C 703 " pdb=" H TYR C 704 " model vdw 1.533 2.270 nonbonded pdb=" O THR C 99 " pdb=" HG1 THR C 103 " model vdw 1.571 2.450 nonbonded pdb=" HH TYR A 229 " pdb=" OD1 ASP B 86 " model vdw 1.577 2.450 nonbonded pdb=" OE1 GLU A 423 " pdb=" H GLU A 423 " model vdw 1.579 2.450 ... (remaining 449198 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.140 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: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.003 0.053 15806 Z= 0.148 Angle : 0.543 7.903 21300 Z= 0.303 Chirality : 0.039 0.229 2333 Planarity : 0.004 0.099 2738 Dihedral : 17.477 89.641 6007 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.11 % Allowed : 25.88 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.35 (0.20), residues: 1938 helix: 1.51 (0.18), residues: 823 sheet: -0.77 (0.35), residues: 230 loop : -0.68 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 484 TYR 0.021 0.001 TYR C 661 PHE 0.016 0.001 PHE C 57 TRP 0.013 0.001 TRP A 402 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00283 (15806) covalent geometry : angle 0.54338 (21300) hydrogen bonds : bond 0.15069 ( 733) hydrogen bonds : angle 5.99728 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.6322 (ptt) cc_final: 0.6081 (ptm) REVERT: A 529 ASP cc_start: 0.8101 (t0) cc_final: 0.7695 (m-30) REVERT: C 545 GLU cc_start: 0.6856 (mm-30) cc_final: 0.5980 (mm-30) outliers start: 36 outliers final: 31 residues processed: 240 average time/residue: 1.0327 time to fit residues: 279.5781 Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 557 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 444 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.196179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149166 restraints weight = 48479.990| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.29 r_work: 0.3588 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15806 Z= 0.160 Angle : 0.528 5.458 21300 Z= 0.279 Chirality : 0.040 0.155 2333 Planarity : 0.004 0.050 2738 Dihedral : 5.973 79.257 2147 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.29 % Allowed : 24.12 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.12 (0.19), residues: 1938 helix: 1.31 (0.18), residues: 827 sheet: -0.90 (0.33), residues: 244 loop : -0.79 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 601 TYR 0.015 0.002 TYR B 466 PHE 0.015 0.001 PHE B 550 TRP 0.014 0.001 TRP A 402 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00370 (15806) covalent geometry : angle 0.52821 (21300) hydrogen bonds : bond 0.04376 ( 733) hydrogen bonds : angle 4.94751 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.6414 (ptt) cc_final: 0.6186 (ptm) REVERT: A 633 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7775 (mt) REVERT: B 453 LYS cc_start: 0.8115 (pttm) cc_final: 0.7915 (ptpt) REVERT: B 526 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.6979 (mpm) REVERT: C 446 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5321 (t0) REVERT: C 545 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6059 (mm-30) outliers start: 56 outliers final: 35 residues processed: 245 average time/residue: 1.1745 time to fit residues: 324.0490 Evaluate side-chains 232 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 38 optimal weight: 0.0470 chunk 100 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150575 restraints weight = 48383.097| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.27 r_work: 0.3572 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15806 Z= 0.136 Angle : 0.496 5.961 21300 Z= 0.260 Chirality : 0.039 0.150 2333 Planarity : 0.004 0.070 2738 Dihedral : 5.422 76.623 2133 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.35 % Allowed : 24.00 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.14 (0.19), residues: 1938 helix: 1.42 (0.18), residues: 826 sheet: -0.98 (0.34), residues: 235 loop : -0.86 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 484 TYR 0.014 0.001 TYR B 466 PHE 0.012 0.001 PHE B 550 TRP 0.013 0.001 TRP A 402 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00313 (15806) covalent geometry : angle 0.49551 (21300) hydrogen bonds : bond 0.03941 ( 733) hydrogen bonds : angle 4.64822 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.6314 (ptt) cc_final: 0.6108 (ptm) REVERT: A 529 ASP cc_start: 0.8094 (t0) cc_final: 0.7849 (m-30) REVERT: A 633 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 526 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.6610 (mpm) REVERT: C 545 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6130 (mm-30) REVERT: C 740 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7815 (ttmm) outliers start: 57 outliers final: 30 residues processed: 252 average time/residue: 1.2083 time to fit residues: 342.3358 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 660 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 89 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148737 restraints weight = 48353.511| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.22 r_work: 0.3561 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15806 Z= 0.157 Angle : 0.512 6.090 21300 Z= 0.269 Chirality : 0.039 0.150 2333 Planarity : 0.004 0.079 2738 Dihedral : 5.232 74.280 2127 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.35 % Allowed : 23.30 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.00 (0.19), residues: 1938 helix: 1.34 (0.18), residues: 826 sheet: -0.96 (0.33), residues: 240 loop : -1.00 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 484 TYR 0.015 0.002 TYR B 466 PHE 0.015 0.001 PHE B 550 TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00368 (15806) covalent geometry : angle 0.51247 (21300) hydrogen bonds : bond 0.03850 ( 733) hydrogen bonds : angle 4.56965 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3078 (mpm) cc_final: 0.2435 (tpp) REVERT: A 277 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6839 (m) REVERT: A 529 ASP cc_start: 0.8080 (t0) cc_final: 0.7852 (m-30) REVERT: A 633 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7675 (mt) REVERT: B 386 ARG cc_start: 0.7350 (ttm110) cc_final: 0.6971 (ttp-110) REVERT: B 444 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7302 (p0) REVERT: B 526 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7438 (mpm) REVERT: C 48 ARG cc_start: 0.6959 (ttt90) cc_final: 0.6374 (ttt-90) REVERT: C 362 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5499 (mm-30) REVERT: C 545 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6182 (mm-30) REVERT: C 740 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7790 (ttmm) outliers start: 57 outliers final: 32 residues processed: 253 average time/residue: 1.1131 time to fit residues: 317.4114 Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 17 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.194070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146770 restraints weight = 48363.698| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.17 r_work: 0.3572 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15806 Z= 0.177 Angle : 0.526 6.121 21300 Z= 0.277 Chirality : 0.040 0.152 2333 Planarity : 0.005 0.080 2738 Dihedral : 5.183 72.010 2123 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.99 % Allowed : 22.83 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: -0.16 (0.19), residues: 1938 helix: 1.15 (0.18), residues: 833 sheet: -1.02 (0.31), residues: 260 loop : -1.05 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 484 TYR 0.017 0.002 TYR B 466 PHE 0.016 0.001 PHE B 550 TRP 0.015 0.002 TRP A 402 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00417 (15806) covalent geometry : angle 0.52564 (21300) hydrogen bonds : bond 0.03936 ( 733) hydrogen bonds : angle 4.57567 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2948 (mpm) cc_final: 0.2298 (tpp) REVERT: A 277 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.6913 (m) REVERT: A 352 MET cc_start: 0.6676 (tpt) cc_final: 0.6373 (tpp) REVERT: A 473 MET cc_start: 0.5603 (ptm) cc_final: 0.5215 (ptm) REVERT: A 565 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 633 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 386 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7161 (ttp-110) REVERT: C 48 ARG cc_start: 0.6983 (ttt90) cc_final: 0.6404 (ttt-90) REVERT: C 362 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5401 (mm-30) REVERT: C 363 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6704 (mt-10) REVERT: C 532 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: C 545 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6340 (mm-30) REVERT: C 740 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7794 (ttmm) outliers start: 68 outliers final: 38 residues processed: 264 average time/residue: 1.2082 time to fit residues: 356.7627 Evaluate side-chains 246 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 532 TYR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 614 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.193290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145953 restraints weight = 48227.993| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.16 r_work: 0.3545 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15806 Z= 0.185 Angle : 0.535 6.183 21300 Z= 0.282 Chirality : 0.040 0.151 2333 Planarity : 0.005 0.082 2738 Dihedral : 5.084 70.965 2119 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.05 % Allowed : 23.18 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: -0.26 (0.19), residues: 1938 helix: 1.09 (0.18), residues: 833 sheet: -1.10 (0.31), residues: 254 loop : -1.11 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 484 TYR 0.016 0.002 TYR B 466 PHE 0.016 0.002 PHE B 550 TRP 0.016 0.002 TRP A 402 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00436 (15806) covalent geometry : angle 0.53471 (21300) hydrogen bonds : bond 0.03952 ( 733) hydrogen bonds : angle 4.58546 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2953 (mpm) cc_final: 0.2358 (tpp) REVERT: A 352 MET cc_start: 0.6833 (tpt) cc_final: 0.6520 (tpp) REVERT: A 392 LYS cc_start: 0.8374 (mptp) cc_final: 0.8155 (tptp) REVERT: A 473 MET cc_start: 0.5594 (ptm) cc_final: 0.5261 (ptm) REVERT: A 633 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7629 (mt) REVERT: B 386 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7234 (ttp-110) REVERT: C 48 ARG cc_start: 0.6917 (ttt90) cc_final: 0.6328 (ttt-90) REVERT: C 362 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5524 (mm-30) REVERT: C 532 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: C 545 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6271 (mm-30) REVERT: C 740 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7820 (ttmm) outliers start: 69 outliers final: 46 residues processed: 260 average time/residue: 1.2690 time to fit residues: 369.7807 Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 532 TYR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 0.3980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.194183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146943 restraints weight = 48203.624| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.17 r_work: 0.3564 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15806 Z= 0.145 Angle : 0.514 6.761 21300 Z= 0.269 Chirality : 0.039 0.148 2333 Planarity : 0.005 0.090 2738 Dihedral : 4.965 70.524 2118 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.58 % Allowed : 23.65 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: -0.12 (0.19), residues: 1938 helix: 1.23 (0.18), residues: 833 sheet: -1.07 (0.32), residues: 254 loop : -1.05 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 484 TYR 0.014 0.001 TYR B 466 PHE 0.013 0.001 PHE B 550 TRP 0.016 0.001 TRP A 402 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00342 (15806) covalent geometry : angle 0.51366 (21300) hydrogen bonds : bond 0.03676 ( 733) hydrogen bonds : angle 4.47115 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3002 (mpm) cc_final: 0.2436 (tpp) REVERT: A 352 MET cc_start: 0.6768 (tpt) cc_final: 0.6466 (tpp) REVERT: A 392 LYS cc_start: 0.8382 (mptp) cc_final: 0.8116 (tptp) REVERT: A 473 MET cc_start: 0.5566 (ptm) cc_final: 0.5262 (ptm) REVERT: A 633 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7615 (mt) REVERT: B 386 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7263 (ttp-110) REVERT: B 526 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7145 (mpm) REVERT: C 48 ARG cc_start: 0.6930 (ttt90) cc_final: 0.5903 (ttm110) REVERT: C 66 MET cc_start: 0.8037 (mmt) cc_final: 0.7799 (mmt) REVERT: C 362 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5524 (mm-30) REVERT: C 532 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: C 545 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6226 (mm-30) REVERT: C 740 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7831 (ttmm) outliers start: 61 outliers final: 42 residues processed: 262 average time/residue: 1.2163 time to fit residues: 357.8029 Evaluate side-chains 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 532 TYR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 608 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 176 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 566 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148624 restraints weight = 48366.968| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.20 r_work: 0.3591 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15806 Z= 0.121 Angle : 0.501 6.538 21300 Z= 0.262 Chirality : 0.038 0.151 2333 Planarity : 0.004 0.095 2738 Dihedral : 4.857 70.162 2118 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.82 % Allowed : 24.53 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.01 (0.19), residues: 1938 helix: 1.37 (0.18), residues: 833 sheet: -1.07 (0.33), residues: 234 loop : -1.01 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 484 TYR 0.016 0.001 TYR C 661 PHE 0.014 0.001 PHE B 181 TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00286 (15806) covalent geometry : angle 0.50142 (21300) hydrogen bonds : bond 0.03448 ( 733) hydrogen bonds : angle 4.36127 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2994 (mpm) cc_final: 0.2462 (tpp) REVERT: A 352 MET cc_start: 0.6759 (tpt) cc_final: 0.6467 (tpp) REVERT: A 392 LYS cc_start: 0.8374 (mptp) cc_final: 0.8099 (tptp) REVERT: A 406 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: A 473 MET cc_start: 0.5559 (ptm) cc_final: 0.5244 (ptm) REVERT: A 633 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7596 (mt) REVERT: B 386 ARG cc_start: 0.7546 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: B 526 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6947 (mpm) REVERT: C 48 ARG cc_start: 0.6872 (ttt90) cc_final: 0.5869 (ttm110) REVERT: C 545 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6130 (mm-30) REVERT: C 740 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7797 (ttmm) outliers start: 48 outliers final: 34 residues processed: 248 average time/residue: 1.2915 time to fit residues: 358.2625 Evaluate side-chains 239 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 594 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 93 optimal weight: 0.4980 chunk 165 optimal weight: 0.5980 chunk 25 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 566 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.195303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148747 restraints weight = 48225.519| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.18 r_work: 0.3598 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15806 Z= 0.115 Angle : 0.500 6.947 21300 Z= 0.260 Chirality : 0.038 0.149 2333 Planarity : 0.005 0.099 2738 Dihedral : 4.767 69.347 2118 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.82 % Allowed : 24.71 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.11 (0.19), residues: 1938 helix: 1.44 (0.18), residues: 835 sheet: -0.96 (0.33), residues: 239 loop : -0.97 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 484 TYR 0.013 0.001 TYR B 466 PHE 0.014 0.001 PHE B 181 TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00272 (15806) covalent geometry : angle 0.50009 (21300) hydrogen bonds : bond 0.03356 ( 733) hydrogen bonds : angle 4.29160 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2824 (mpm) cc_final: 0.2328 (tpp) REVERT: A 282 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (t80) REVERT: A 352 MET cc_start: 0.6836 (tpt) cc_final: 0.6544 (tpp) REVERT: A 392 LYS cc_start: 0.8374 (mptp) cc_final: 0.8075 (tptp) REVERT: A 406 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: A 473 MET cc_start: 0.5584 (ptm) cc_final: 0.5243 (ptm) REVERT: A 633 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7594 (mt) REVERT: B 386 ARG cc_start: 0.7567 (ttm110) cc_final: 0.7234 (ttp-110) REVERT: B 526 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.6850 (mpm) REVERT: C 48 ARG cc_start: 0.6838 (ttt90) cc_final: 0.5825 (ttm110) REVERT: C 363 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6391 (mt-10) REVERT: C 545 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6115 (mm-30) REVERT: C 740 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7787 (ttmm) outliers start: 48 outliers final: 36 residues processed: 244 average time/residue: 1.3837 time to fit residues: 376.7594 Evaluate side-chains 242 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147773 restraints weight = 48009.873| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.15 r_work: 0.3582 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15806 Z= 0.136 Angle : 0.518 8.929 21300 Z= 0.270 Chirality : 0.039 0.154 2333 Planarity : 0.004 0.078 2738 Dihedral : 4.770 68.502 2117 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.52 % Allowed : 24.77 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.07 (0.19), residues: 1938 helix: 1.41 (0.18), residues: 835 sheet: -0.95 (0.33), residues: 240 loop : -1.00 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 601 TYR 0.014 0.001 TYR B 466 PHE 0.018 0.001 PHE B 181 TRP 0.015 0.001 TRP A 402 HIS 0.006 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00322 (15806) covalent geometry : angle 0.51793 (21300) hydrogen bonds : bond 0.03482 ( 733) hydrogen bonds : angle 4.30595 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2703 (mpm) cc_final: 0.2278 (tpp) REVERT: A 352 MET cc_start: 0.6954 (tpt) cc_final: 0.6653 (tpp) REVERT: A 392 LYS cc_start: 0.8376 (mptp) cc_final: 0.8091 (tptp) REVERT: A 406 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: A 473 MET cc_start: 0.5609 (ptm) cc_final: 0.5265 (ptm) REVERT: A 633 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7603 (mt) REVERT: B 386 ARG cc_start: 0.7579 (ttm110) cc_final: 0.7232 (ttp-110) REVERT: B 410 MET cc_start: 0.6915 (mtt) cc_final: 0.6686 (mtm) REVERT: B 526 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7238 (mpm) REVERT: C 48 ARG cc_start: 0.6820 (ttt90) cc_final: 0.5809 (ttm110) REVERT: C 363 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6400 (mt-10) REVERT: C 545 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6228 (mm-30) REVERT: C 740 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7790 (ttmm) outliers start: 43 outliers final: 37 residues processed: 248 average time/residue: 1.4272 time to fit residues: 394.3276 Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.193687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146783 restraints weight = 48339.593| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.21 r_work: 0.3568 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15806 Z= 0.150 Angle : 0.527 8.392 21300 Z= 0.276 Chirality : 0.039 0.156 2333 Planarity : 0.005 0.098 2738 Dihedral : 4.779 68.023 2116 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.52 % Allowed : 24.88 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: -0.01 (0.19), residues: 1938 helix: 1.33 (0.18), residues: 835 sheet: -0.98 (0.33), residues: 240 loop : -1.02 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 484 TYR 0.014 0.001 TYR B 466 PHE 0.019 0.001 PHE B 181 TRP 0.014 0.001 TRP A 402 HIS 0.007 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00357 (15806) covalent geometry : angle 0.52704 (21300) hydrogen bonds : bond 0.03599 ( 733) hydrogen bonds : angle 4.35253 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11356.85 seconds wall clock time: 192 minutes 37.81 seconds (11557.81 seconds total)