Starting phenix.real_space_refine on Thu Jun 26 23:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn2_19384/06_2025/8rn2_19384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn2_19384/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn2_19384/06_2025/8rn2_19384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn2_19384/06_2025/8rn2_19384.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn2_19384/06_2025/8rn2_19384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn2_19384/06_2025/8rn2_19384.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.00, per 1000 atoms: 0.51 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: 7.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.62 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: 13.48 Time building geometry restraints manager: 9.57 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: 6.760 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: 0.490 Extract box with map and model: 1.250 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 68.500 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP A 402 HIS 0.002 0.001 HIS A 41 PHE 0.016 0.001 PHE C 57 TYR 0.021 0.001 TYR C 661 ARG 0.016 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.15069 ( 733) hydrogen bonds : angle 5.99728 ( 2058) covalent geometry : bond 0.00283 (15806) covalent geometry : angle 0.54338 (21300) *********************** 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 : 2.324 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: 2.3068 time to fit residues: 628.1834 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 : 2.364 ------------------------------------------------------------------------------- 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 163 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 113 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.196901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150690 restraints weight = 48154.314| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.31 r_work: 0.3607 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0716 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= 0.140 Angle : 0.514 5.311 21300 Z= 0.271 Chirality : 0.039 0.153 2333 Planarity : 0.004 0.051 2738 Dihedral : 5.897 79.740 2147 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.93 % Allowed : 24.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1938 helix: 1.41 (0.18), residues: 827 sheet: -0.86 (0.33), residues: 244 loop : -0.73 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 PHE 0.013 0.001 PHE B 550 TYR 0.014 0.001 TYR B 466 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 733) hydrogen bonds : angle 4.90602 ( 2058) covalent geometry : bond 0.00319 (15806) covalent geometry : angle 0.51395 (21300) *********************** 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 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.529 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 473 MET cc_start: 0.6333 (ptt) cc_final: 0.6125 (ptm) REVERT: A 633 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7762 (mt) REVERT: B 526 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.6698 (mpm) REVERT: C 446 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5379 (t0) REVERT: C 545 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6028 (mm-30) outliers start: 50 outliers final: 31 residues processed: 243 average time/residue: 2.3199 time to fit residues: 639.0945 Evaluate side-chains 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 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 492 THR Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 136 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 480 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 660 SER 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 8 optimal weight: 7.9990 chunk 147 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.196342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149342 restraints weight = 48485.727| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.33 r_work: 0.3586 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15806 Z= 0.141 Angle : 0.499 6.125 21300 Z= 0.262 Chirality : 0.039 0.151 2333 Planarity : 0.004 0.077 2738 Dihedral : 5.270 76.726 2130 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.46 % Allowed : 23.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1938 helix: 1.44 (0.18), residues: 826 sheet: -0.96 (0.34), residues: 235 loop : -0.85 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS B 47 PHE 0.013 0.001 PHE B 550 TYR 0.015 0.001 TYR B 466 ARG 0.008 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 733) hydrogen bonds : angle 4.66099 ( 2058) covalent geometry : bond 0.00329 (15806) covalent geometry : angle 0.49921 (21300) *********************** 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 266 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 2.847 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: 0.6318 (ptt) cc_final: 0.6108 (ptm) REVERT: A 529 ASP cc_start: 0.8097 (t0) cc_final: 0.7858 (m-30) REVERT: A 633 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 526 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7049 (mpm) REVERT: C 446 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5418 (t0) REVERT: C 545 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6120 (mm-30) outliers start: 59 outliers final: 31 residues processed: 251 average time/residue: 2.4629 time to fit residues: 696.1430 Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 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 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 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 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 44 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** B 346 ASN B 429 ASN C 636 GLN C 692 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.193268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144914 restraints weight = 48478.641| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.17 r_work: 0.3515 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15806 Z= 0.212 Angle : 0.562 6.193 21300 Z= 0.297 Chirality : 0.041 0.156 2333 Planarity : 0.005 0.080 2738 Dihedral : 5.442 72.718 2127 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.05 % Allowed : 22.71 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1938 helix: 1.05 (0.18), residues: 826 sheet: -1.11 (0.32), residues: 247 loop : -1.09 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.003 0.001 HIS A 643 PHE 0.018 0.002 PHE B 550 TYR 0.019 0.002 TYR B 466 ARG 0.008 0.001 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 733) hydrogen bonds : angle 4.75389 ( 2058) covalent geometry : bond 0.00497 (15806) covalent geometry : angle 0.56166 (21300) *********************** 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 279 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 2.682 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: 0.2952 (mpm) cc_final: 0.2358 (tpp) REVERT: A 277 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.6861 (m) REVERT: A 460 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 473 MET cc_start: 0.6327 (ptt) cc_final: 0.6125 (ptm) REVERT: A 529 ASP cc_start: 0.8121 (t0) cc_final: 0.7899 (m-30) REVERT: A 633 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7667 (mt) REVERT: B 386 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7248 (ttm110) REVERT: C 48 ARG cc_start: 0.7040 (ttt90) cc_final: 0.6499 (ttt-90) REVERT: C 362 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5472 (mm-30) REVERT: C 446 ASP cc_start: 0.5788 (OUTLIER) cc_final: 0.5441 (t0) REVERT: C 545 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6267 (mm-30) REVERT: C 740 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7799 (ttmm) outliers start: 69 outliers final: 35 residues processed: 264 average time/residue: 2.6253 time to fit residues: 779.9329 Evaluate side-chains 237 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 460 LEU 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 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 348 ILE Chi-restraints excluded: chain C residue 362 GLU 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 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 35 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147020 restraints weight = 48217.423| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.22 r_work: 0.3585 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15806 Z= 0.143 Angle : 0.512 6.179 21300 Z= 0.269 Chirality : 0.039 0.148 2333 Planarity : 0.004 0.077 2738 Dihedral : 5.245 72.685 2125 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.35 % Allowed : 23.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1938 helix: 1.20 (0.18), residues: 828 sheet: -1.10 (0.32), residues: 255 loop : -1.02 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.003 0.001 HIS C 235 PHE 0.014 0.001 PHE B 550 TYR 0.014 0.001 TYR B 466 ARG 0.010 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 733) hydrogen bonds : angle 4.57067 ( 2058) covalent geometry : bond 0.00334 (15806) covalent geometry : angle 0.51179 (21300) *********************** 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 266 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 2.752 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: A 1 MET cc_start: 0.3046 (mpm) cc_final: 0.2391 (tpp) REVERT: A 277 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.6902 (m) REVERT: A 332 ASN cc_start: 0.6809 (p0) cc_final: 0.6164 (p0) REVERT: A 352 MET cc_start: 0.6596 (tpt) cc_final: 0.6254 (tpp) REVERT: A 633 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mt) REVERT: B 386 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7252 (ttm110) REVERT: C 48 ARG cc_start: 0.6964 (ttt90) cc_final: 0.6378 (ttt-90) REVERT: C 362 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5536 (mm-30) REVERT: C 446 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5519 (t0) REVERT: C 545 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6217 (mm-30) REVERT: C 740 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7811 (ttmm) outliers start: 57 outliers final: 37 residues processed: 252 average time/residue: 2.3722 time to fit residues: 673.1030 Evaluate side-chains 239 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 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 277 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 ILE 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 298 SER 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 446 ASP 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 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 127 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.195569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148303 restraints weight = 48450.899| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.20 r_work: 0.3595 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15806 Z= 0.120 Angle : 0.491 6.545 21300 Z= 0.257 Chirality : 0.038 0.146 2333 Planarity : 0.004 0.086 2738 Dihedral : 5.094 72.245 2125 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.29 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1938 helix: 1.36 (0.18), residues: 832 sheet: -0.97 (0.33), residues: 239 loop : -1.04 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 550 TYR 0.013 0.001 TYR B 466 ARG 0.012 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 733) hydrogen bonds : angle 4.42579 ( 2058) covalent geometry : bond 0.00282 (15806) covalent geometry : angle 0.49127 (21300) *********************** 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 270 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 2.657 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: 0.2947 (mpm) cc_final: 0.2361 (tpp) REVERT: A 352 MET cc_start: 0.6622 (tpt) cc_final: 0.6290 (tpp) REVERT: A 473 MET cc_start: 0.5566 (ptm) cc_final: 0.5224 (ptm) REVERT: A 633 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7602 (mt) REVERT: B 386 ARG cc_start: 0.7517 (ttm110) cc_final: 0.7179 (ttp-110) REVERT: B 444 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7190 (p0) REVERT: B 526 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7095 (mpm) REVERT: C 48 ARG cc_start: 0.6931 (ttt90) cc_final: 0.5860 (ttm110) REVERT: C 66 MET cc_start: 0.8048 (mmt) cc_final: 0.7796 (mmt) REVERT: C 446 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5585 (t0) REVERT: C 545 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6234 (mm-30) REVERT: C 740 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7787 (ttmm) outliers start: 56 outliers final: 33 residues processed: 255 average time/residue: 2.5522 time to fit residues: 726.7325 Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 478 VAL Chi-restraints excluded: chain A residue 517 VAL 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 328 ASP Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 444 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 289 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 298 SER 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 446 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 121 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.193071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145468 restraints weight = 48408.628| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.19 r_work: 0.3561 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15806 Z= 0.195 Angle : 0.547 6.240 21300 Z= 0.288 Chirality : 0.040 0.147 2333 Planarity : 0.005 0.093 2738 Dihedral : 5.057 70.511 2118 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.40 % Allowed : 24.06 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1938 helix: 1.08 (0.18), residues: 833 sheet: -1.08 (0.31), residues: 259 loop : -1.15 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.003 0.001 HIS C 463 PHE 0.017 0.002 PHE B 550 TYR 0.017 0.002 TYR B 466 ARG 0.011 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 733) hydrogen bonds : angle 4.57099 ( 2058) covalent geometry : bond 0.00461 (15806) covalent geometry : angle 0.54691 (21300) *********************** 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 261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 2.667 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 1 MET cc_start: 0.3009 (mpm) cc_final: 0.2438 (tpp) REVERT: A 332 ASN cc_start: 0.6973 (p0) cc_final: 0.6333 (p0) REVERT: A 352 MET cc_start: 0.6649 (tpt) cc_final: 0.6334 (tpp) REVERT: A 392 LYS cc_start: 0.8380 (mptp) cc_final: 0.8118 (tptp) REVERT: A 473 MET cc_start: 0.5586 (ptm) cc_final: 0.5284 (ptm) REVERT: A 633 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7623 (mt) REVERT: B 386 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7198 (ttp-110) REVERT: C 48 ARG cc_start: 0.6914 (ttt90) cc_final: 0.5873 (ttm110) REVERT: C 362 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5509 (mm-30) REVERT: C 446 ASP cc_start: 0.5962 (OUTLIER) cc_final: 0.5587 (t0) REVERT: C 545 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6290 (mm-30) REVERT: C 740 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7817 (ttmm) outliers start: 58 outliers final: 40 residues processed: 249 average time/residue: 2.5763 time to fit residues: 716.9302 Evaluate side-chains 240 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 2.544 ------------------------------------------------------------------------------- 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 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 517 VAL 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 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 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 446 ASP 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 Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 667 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 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 = 0.4290 r_free = 0.4290 target = 0.193480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146621 restraints weight = 48457.639| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.18 r_work: 0.3561 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15806 Z= 0.150 Angle : 0.520 6.771 21300 Z= 0.273 Chirality : 0.039 0.148 2333 Planarity : 0.005 0.094 2738 Dihedral : 4.975 70.357 2118 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 24.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1938 helix: 1.19 (0.18), residues: 833 sheet: -1.07 (0.31), residues: 259 loop : -1.12 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS C 463 PHE 0.014 0.001 PHE B 181 TYR 0.014 0.001 TYR B 466 ARG 0.014 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 733) hydrogen bonds : angle 4.46722 ( 2058) covalent geometry : bond 0.00352 (15806) covalent geometry : angle 0.51971 (21300) *********************** 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 256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 2.531 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: A 1 MET cc_start: 0.3007 (mpm) cc_final: 0.2479 (tpp) REVERT: A 332 ASN cc_start: 0.6827 (p0) cc_final: 0.6100 (p0) REVERT: A 352 MET cc_start: 0.6640 (tpt) cc_final: 0.6320 (tpp) REVERT: A 392 LYS cc_start: 0.8379 (mptp) cc_final: 0.8109 (tptp) REVERT: A 473 MET cc_start: 0.5647 (ptm) cc_final: 0.5334 (ptm) REVERT: A 633 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 386 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7258 (ttp-110) REVERT: C 48 ARG cc_start: 0.6899 (ttt90) cc_final: 0.5888 (ttm110) REVERT: C 362 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5536 (mm-30) REVERT: C 446 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5589 (t0) REVERT: C 545 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6215 (mm-30) REVERT: C 740 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7818 (ttmm) outliers start: 52 outliers final: 42 residues processed: 245 average time/residue: 2.4997 time to fit residues: 685.4719 Evaluate side-chains 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 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 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 21 THR 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 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 446 ASP 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 Chi-restraints excluded: chain C residue 608 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.193426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146634 restraints weight = 48158.436| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.15 r_work: 0.3577 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15806 Z= 0.148 Angle : 0.520 6.809 21300 Z= 0.273 Chirality : 0.039 0.155 2333 Planarity : 0.005 0.100 2738 Dihedral : 4.947 69.769 2118 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.29 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1938 helix: 1.21 (0.18), residues: 835 sheet: -1.07 (0.33), residues: 234 loop : -1.10 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS C 463 PHE 0.016 0.001 PHE B 181 TYR 0.014 0.001 TYR B 466 ARG 0.015 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 733) hydrogen bonds : angle 4.44503 ( 2058) covalent geometry : bond 0.00350 (15806) covalent geometry : angle 0.51993 (21300) *********************** 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 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 2.613 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: 0.2781 (mpm) cc_final: 0.2309 (tpp) REVERT: A 332 ASN cc_start: 0.6732 (p0) cc_final: 0.6007 (p0) REVERT: A 352 MET cc_start: 0.6737 (tpt) cc_final: 0.6413 (tpp) REVERT: A 392 LYS cc_start: 0.8395 (mptp) cc_final: 0.8102 (tptp) REVERT: A 473 MET cc_start: 0.5648 (ptm) cc_final: 0.5354 (ptm) REVERT: A 633 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7607 (mt) REVERT: B 386 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7269 (ttp-110) REVERT: B 526 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7426 (mpm) REVERT: C 48 ARG cc_start: 0.6845 (ttt90) cc_final: 0.5824 (ttm110) REVERT: C 66 MET cc_start: 0.8019 (mmt) cc_final: 0.7774 (mmt) REVERT: C 362 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5543 (mm-30) REVERT: C 446 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5689 (t0) REVERT: C 545 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6233 (mm-30) REVERT: C 740 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7804 (ttmm) outliers start: 56 outliers final: 43 residues processed: 251 average time/residue: 2.5156 time to fit residues: 708.7998 Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 MET 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 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 21 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 156 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 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 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 446 ASP 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 Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 182 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.194369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148409 restraints weight = 48144.174| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.20 r_work: 0.3589 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15806 Z= 0.124 Angle : 0.510 7.050 21300 Z= 0.267 Chirality : 0.038 0.152 2333 Planarity : 0.005 0.103 2738 Dihedral : 4.877 69.620 2118 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.76 % Allowed : 24.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1938 helix: 1.33 (0.18), residues: 835 sheet: -1.04 (0.33), residues: 234 loop : -1.05 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.006 0.001 HIS C 463 PHE 0.016 0.001 PHE B 181 TYR 0.013 0.001 TYR B 466 ARG 0.015 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 733) hydrogen bonds : angle 4.36836 ( 2058) covalent geometry : bond 0.00292 (15806) covalent geometry : angle 0.51033 (21300) ********************** 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 253 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 2.272 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: 0.2712 (mpm) cc_final: 0.2290 (tpp) REVERT: A 332 ASN cc_start: 0.6686 (p0) cc_final: 0.5911 (p0) REVERT: A 352 MET cc_start: 0.6732 (tpt) cc_final: 0.6420 (tpp) REVERT: A 392 LYS cc_start: 0.8384 (mptp) cc_final: 0.8106 (tptp) REVERT: A 473 MET cc_start: 0.5655 (ptm) cc_final: 0.5335 (ptm) REVERT: A 633 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7613 (mt) REVERT: B 386 ARG cc_start: 0.7569 (ttm110) cc_final: 0.7217 (ttp-110) REVERT: B 410 MET cc_start: 0.6929 (mtt) cc_final: 0.6671 (mtm) REVERT: B 526 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7033 (mpm) REVERT: C 48 ARG cc_start: 0.6835 (ttt90) cc_final: 0.5829 (ttm110) REVERT: C 66 MET cc_start: 0.8028 (mmt) cc_final: 0.7801 (mmt) REVERT: C 446 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5681 (t0) REVERT: C 545 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6220 (mm-30) REVERT: C 740 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7804 (ttmm) outliers start: 47 outliers final: 37 residues processed: 241 average time/residue: 2.6374 time to fit residues: 709.6606 Evaluate side-chains 240 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 MET 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 478 VAL Chi-restraints excluded: chain A residue 517 VAL 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 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 328 ASP 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 446 ASP 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 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 169 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4291 r_free = 0.4291 target = 0.193573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147788 restraints weight = 48298.094| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.21 r_work: 0.3572 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15806 Z= 0.149 Angle : 0.521 6.852 21300 Z= 0.273 Chirality : 0.039 0.156 2333 Planarity : 0.005 0.106 2738 Dihedral : 4.900 68.719 2118 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.58 % Allowed : 25.06 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1938 helix: 1.26 (0.18), residues: 835 sheet: -1.06 (0.33), residues: 234 loop : -1.08 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.008 0.001 HIS C 463 PHE 0.017 0.001 PHE B 181 TYR 0.014 0.001 TYR B 466 ARG 0.014 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 733) hydrogen bonds : angle 4.39208 ( 2058) covalent geometry : bond 0.00352 (15806) covalent geometry : angle 0.52124 (21300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24127.95 seconds wall clock time: 410 minutes 46.25 seconds (24646.25 seconds total)