Starting phenix.real_space_refine on Sun Aug 9 05:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn1_19383/08_2026/8rn1_19383.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 121 5.16 5 C 10401 2.51 5 N 2824 2.21 5 O 3106 1.98 5 H 16438 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32902 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11305 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 11304 Classifications: {'peptide': 705} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 705, 11304 Classifications: {'peptide': 705} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 1 bond proxies already assigned to first conformer: 11419 Chain: "B" Number of atoms: 9959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 9959 Classifications: {'peptide': 637} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 604} Chain breaks: 2 Chain: "V" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 397 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "C" Number of atoms: 11241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 11241 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain breaks: 1 Time building chain proxies: 5.84, per 1000 atoms: 0.18 Number of scatterers: 32902 At special positions: 0 Unit cell: (129.944, 107.994, 140.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 P 12 15.00 O 3106 8.00 N 2824 7.00 C 10401 6.00 H 16438 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 25 sheets defined 48.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.762A pdb=" N ARG A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 31 through 48 removed outlier: 4.351A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.701A pdb=" N LYS A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.202A 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: 3.674A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.130A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 596 removed outlier: 4.094A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (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 670 removed outlier: 4.250A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.131A 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 715 removed outlier: 3.755A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.019A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 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 125 removed outlier: 3.593A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.623A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.755A 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 248 through 265 removed outlier: 3.873A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.411A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 377 through 381 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 426 Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 518 through 535 removed outlier: 3.619A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.957A 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 613 removed outlier: 4.553A pdb=" N ASN B 613 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 removed outlier: 4.636A pdb=" N ARG B 622 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.647A pdb=" N LYS B 640 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 51 removed outlier: 4.099A pdb=" N MET C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 51' Processing helix chain 'C' and resid 64 through 70 removed outlier: 4.427A pdb=" N ILE C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.936A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.817A pdb=" N GLN C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 275 removed outlier: 3.571A pdb=" N VAL C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.961A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.677A pdb=" N CYS C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.588A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) 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 452 removed outlier: 3.972A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 4.054A pdb=" N VAL C 519 " --> pdb=" O ALA C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 541 removed outlier: 3.841A pdb=" N MET C 537 " --> pdb=" O THR C 534 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU C 539 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.595A pdb=" N LEU C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 568 " --> pdb=" O GLN C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.555A pdb=" N GLN C 574 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.293A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.159A 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: 4.185A 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 688 Processing helix chain 'C' and resid 713 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 4.761A pdb=" N ARG A 74 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.611A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.806A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.644A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG A 540 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 324 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.644A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.869A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 628 removed outlier: 5.914A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 184 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.639A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 491 removed outlier: 6.978A pdb=" N PHE B 495 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.425A pdb=" N GLN C 91 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB6, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.676A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 146 Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC1, first strand: chain 'C' and resid 334 through 337 removed outlier: 6.853A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS C 385 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 340 through 347 removed outlier: 3.847A pdb=" N ILE C 346 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 354 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AC4, first strand: chain 'C' and resid 498 through 499 removed outlier: 3.534A pdb=" N SER C 498 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 505 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC6, first strand: chain 'C' and resid 660 through 662 Processing sheet with id=AC7, first strand: chain 'C' and resid 698 through 702 removed outlier: 7.417A pdb=" N LYS C 737 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2163 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: 8.57 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16402 1.04 - 1.24: 1131 1.24 - 1.43: 5953 1.43 - 1.63: 9556 1.63 - 1.83: 206 Bond restraints: 33248 Sorted by residual: bond pdb=" C LEU B 508 " pdb=" N PRO B 509 " ideal model delta sigma weight residual 1.328 1.350 -0.022 1.26e-02 6.30e+03 2.98e+00 bond pdb=" CA PRO C 157 " pdb=" C PRO C 157 " ideal model delta sigma weight residual 1.517 1.507 0.010 6.70e-03 2.23e+04 2.22e+00 bond pdb=" C PRO B 509 " pdb=" O PRO B 509 " ideal model delta sigma weight residual 1.232 1.218 0.014 1.31e-02 5.83e+03 1.09e+00 bond pdb=" CA PRO B 509 " pdb=" HA PRO B 509 " ideal model delta sigma weight residual 0.970 0.990 -0.020 2.00e-02 2.50e+03 9.94e-01 bond pdb=" CA PRO B 509 " pdb=" C PRO B 509 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.11e-02 8.12e+03 9.57e-01 ... (remaining 33243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 59763 1.97 - 3.95: 421 3.95 - 5.92: 19 5.92 - 7.90: 3 7.90 - 9.87: 1 Bond angle restraints: 60207 Sorted by residual: angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 113.71 109.98 3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" CB MET B 459 " pdb=" CG MET B 459 " pdb=" SD MET B 459 " ideal model delta sigma weight residual 112.70 122.57 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N GLY A 542 " pdb=" CA GLY A 542 " pdb=" C GLY A 542 " ideal model delta sigma weight residual 111.42 116.26 -4.84 1.51e+00 4.39e-01 1.03e+01 angle pdb=" O5' G V 5 " pdb=" C5' G V 5 " pdb=" C4' G V 5 " ideal model delta sigma weight residual 109.40 111.93 -2.53 8.00e-01 1.56e+00 9.98e+00 angle pdb=" O5' A V 7 " pdb=" C5' A V 7 " pdb=" C4' A V 7 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.58e+00 ... (remaining 60202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13641 17.99 - 35.98: 1337 35.98 - 53.97: 435 53.97 - 71.95: 96 71.95 - 89.94: 22 Dihedral angle restraints: 15531 sinusoidal: 8713 harmonic: 6818 Sorted by residual: dihedral pdb=" CA MET C 690 " pdb=" C MET C 690 " pdb=" N GLY C 691 " pdb=" CA GLY C 691 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA SER A 25 " pdb=" C SER A 25 " pdb=" N GLU A 26 " pdb=" CA GLU A 26 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ARG C 146 " pdb=" C ARG C 146 " pdb=" N VAL C 147 " pdb=" CA VAL C 147 " ideal model delta harmonic sigma weight residual 180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 15528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1651 0.030 - 0.060: 601 0.060 - 0.089: 127 0.089 - 0.119: 102 0.119 - 0.149: 19 Chirality restraints: 2500 Sorted by residual: chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL C 290 " pdb=" N VAL C 290 " pdb=" C VAL C 290 " pdb=" CB VAL C 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL B 208 " pdb=" N VAL B 208 " pdb=" C VAL B 208 " pdb=" CB VAL B 208 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2497 not shown) Planarity restraints: 4827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 31 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO A 32 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 508 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU B 508 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 508 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO B 509 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 74 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 75 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.025 5.00e-02 4.00e+02 ... (remaining 4824 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1044 2.13 - 2.74: 61034 2.74 - 3.36: 96614 3.36 - 3.98: 121068 3.98 - 4.60: 191596 Nonbonded interactions: 471356 Sorted by model distance: nonbonded pdb=" OE1 GLU C 186 " pdb=" H GLU C 186 " model vdw 1.508 2.450 nonbonded pdb=" H GLY B 157 " pdb=" OD2 ASP B 169 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU C 539 " pdb=" H GLU C 539 " model vdw 1.580 2.450 nonbonded pdb=" OE1 GLU A 296 " pdb=" H GLU A 296 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU C 114 " pdb=" H GLU C 114 " model vdw 1.583 2.450 ... (remaining 471351 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 0.029 16810 Z= 0.131 Angle : 0.538 9.874 22713 Z= 0.294 Chirality : 0.038 0.149 2500 Planarity : 0.004 0.079 2871 Dihedral : 16.643 89.944 6475 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.34 % Allowed : 18.49 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2023 helix: 1.33 (0.18), residues: 862 sheet: -0.54 (0.34), residues: 216 loop : -0.63 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 178 TYR 0.013 0.001 TYR B 554 PHE 0.015 0.001 PHE B 511 TRP 0.017 0.001 TRP B 437 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16810) covalent geometry : angle 0.53762 / 0.29 (22713) hydrogen bonds : bond 0.14227 / 9.14 ( 777) hydrogen bonds : angle 6.09365 / 4.26 ( 2163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 370 LEU cc_start: 0.9111 (mt) cc_final: 0.8833 (mt) REVERT: A 437 GLU cc_start: 0.8490 (tt0) cc_final: 0.8227 (tt0) outliers start: 6 outliers final: 5 residues processed: 275 average time/residue: 0.2729 time to fit residues: 115.3536 Evaluate side-chains 265 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 260 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106133 restraints weight = 98926.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110503 restraints weight = 35793.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113051 restraints weight = 19807.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114431 restraints weight = 14450.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114967 restraints weight = 12380.950| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16810 Z= 0.131 Angle : 0.546 8.207 22713 Z= 0.286 Chirality : 0.038 0.165 2500 Planarity : 0.004 0.079 2871 Dihedral : 7.470 82.230 2381 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.84 % Allowed : 18.16 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2023 helix: 1.40 (0.18), residues: 865 sheet: -0.63 (0.33), residues: 212 loop : -0.65 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.012 0.001 TYR B 554 PHE 0.013 0.001 PHE A 36 TRP 0.013 0.001 TRP B 437 HIS 0.002 0.000 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16810) covalent geometry : angle 0.54587 / 0.29 (22713) hydrogen bonds : bond 0.04693 / 2.99 ( 777) hydrogen bonds : angle 5.19022 / 3.57 ( 2163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.9008 (mt) cc_final: 0.8702 (mt) REVERT: A 437 GLU cc_start: 0.8517 (tt0) cc_final: 0.8222 (tt0) REVERT: A 642 MET cc_start: 0.8412 (mmt) cc_final: 0.8168 (mmp) REVERT: B 289 MET cc_start: 0.8889 (mmm) cc_final: 0.8589 (mmm) REVERT: B 601 ARG cc_start: 0.8096 (ptm-80) cc_final: 0.7893 (ptm-80) REVERT: C 183 ILE cc_start: 0.7076 (tt) cc_final: 0.6690 (mt) outliers start: 15 outliers final: 11 residues processed: 268 average time/residue: 0.2750 time to fit residues: 113.2349 Evaluate side-chains 264 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 258 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 148 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101941 restraints weight = 99255.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106182 restraints weight = 36521.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108668 restraints weight = 20468.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110016 restraints weight = 15056.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110711 restraints weight = 12931.221| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16810 Z= 0.205 Angle : 0.550 7.945 22713 Z= 0.291 Chirality : 0.039 0.153 2500 Planarity : 0.004 0.069 2871 Dihedral : 7.472 85.542 2377 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.29 % Allowed : 17.43 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2023 helix: 1.20 (0.17), residues: 884 sheet: -0.79 (0.33), residues: 207 loop : -0.85 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.018 0.001 TYR B 554 PHE 0.015 0.001 PHE A 24 TRP 0.016 0.001 TRP B 437 HIS 0.009 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (16810) covalent geometry : angle 0.54961 / 0.29 (22713) hydrogen bonds : bond 0.04427 / 2.83 ( 777) hydrogen bonds : angle 5.13861 / 3.53 ( 2163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.8542 (tt0) cc_final: 0.8326 (tt0) REVERT: B 276 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6102 (m110) REVERT: B 289 MET cc_start: 0.8867 (mmm) cc_final: 0.8422 (mmm) REVERT: B 585 ARG cc_start: 0.8640 (mpt-90) cc_final: 0.8224 (mtt90) REVERT: C 183 ILE cc_start: 0.7080 (tt) cc_final: 0.6740 (mt) REVERT: C 199 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5984 (mtt) REVERT: C 508 ARG cc_start: 0.8284 (ptp-110) cc_final: 0.7781 (ptp90) outliers start: 23 outliers final: 17 residues processed: 267 average time/residue: 0.2576 time to fit residues: 106.5376 Evaluate side-chains 263 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 369 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 8 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 140 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN B 265 ASN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102668 restraints weight = 98258.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106946 restraints weight = 35817.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109447 restraints weight = 19961.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110796 restraints weight = 14650.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111288 restraints weight = 12573.109| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16810 Z= 0.139 Angle : 0.514 6.107 22713 Z= 0.270 Chirality : 0.038 0.150 2500 Planarity : 0.004 0.069 2871 Dihedral : 7.482 85.813 2377 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.29 % Allowed : 17.65 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2023 helix: 1.29 (0.17), residues: 878 sheet: -0.86 (0.33), residues: 207 loop : -0.82 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 540 TYR 0.014 0.001 TYR B 554 PHE 0.012 0.001 PHE A 24 TRP 0.015 0.001 TRP B 437 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16810) covalent geometry : angle 0.51393 / 0.27 (22713) hydrogen bonds : bond 0.03950 / 2.53 ( 777) hydrogen bonds : angle 4.96363 / 3.40 ( 2163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.829 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 437 GLU cc_start: 0.8527 (tt0) cc_final: 0.8283 (tt0) REVERT: A 591 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7398 (mp0) REVERT: B 289 MET cc_start: 0.8872 (mmm) cc_final: 0.8306 (mmm) REVERT: B 459 MET cc_start: 0.7870 (mmm) cc_final: 0.7555 (mmt) REVERT: C 160 GLU cc_start: 0.6036 (tt0) cc_final: 0.5814 (tt0) REVERT: C 183 ILE cc_start: 0.6924 (tt) cc_final: 0.6695 (mt) REVERT: C 199 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6055 (mtt) REVERT: C 508 ARG cc_start: 0.8284 (ptp-110) cc_final: 0.7775 (ptp90) outliers start: 23 outliers final: 17 residues processed: 271 average time/residue: 0.2927 time to fit residues: 122.6136 Evaluate side-chains 263 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 73 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102765 restraints weight = 99463.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107021 restraints weight = 36173.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109513 restraints weight = 20144.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110862 restraints weight = 14754.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111564 restraints weight = 12657.667| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16810 Z= 0.146 Angle : 0.517 6.133 22713 Z= 0.272 Chirality : 0.038 0.161 2500 Planarity : 0.004 0.066 2871 Dihedral : 7.482 86.705 2377 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.57 % Allowed : 17.20 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2023 helix: 1.27 (0.17), residues: 884 sheet: -0.95 (0.33), residues: 206 loop : -0.83 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 585 TYR 0.015 0.001 TYR B 554 PHE 0.012 0.001 PHE A 24 TRP 0.014 0.001 TRP B 437 HIS 0.012 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16810) covalent geometry : angle 0.51715 / 0.27 (22713) hydrogen bonds : bond 0.03829 / 2.45 ( 777) hydrogen bonds : angle 4.88740 / 3.35 ( 2163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.887 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 36 PHE cc_start: 0.8603 (m-80) cc_final: 0.8216 (m-80) REVERT: A 437 GLU cc_start: 0.8568 (tt0) cc_final: 0.8332 (tt0) REVERT: A 591 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7397 (mp0) REVERT: B 289 MET cc_start: 0.8901 (mmm) cc_final: 0.8243 (mmm) REVERT: B 459 MET cc_start: 0.7864 (mmm) cc_final: 0.7556 (mmt) REVERT: C 199 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.6091 (mtt) REVERT: C 236 CYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8617 (m) REVERT: C 508 ARG cc_start: 0.8285 (ptp-110) cc_final: 0.7789 (ptp90) REVERT: C 716 GLU cc_start: 0.7026 (pt0) cc_final: 0.6820 (pt0) outliers start: 28 outliers final: 19 residues processed: 268 average time/residue: 0.2731 time to fit residues: 113.3381 Evaluate side-chains 263 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN A 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103259 restraints weight = 98458.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107558 restraints weight = 35783.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110054 restraints weight = 19880.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111250 restraints weight = 14562.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112054 restraints weight = 12660.174| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16810 Z= 0.115 Angle : 0.502 6.215 22713 Z= 0.262 Chirality : 0.038 0.150 2500 Planarity : 0.004 0.065 2871 Dihedral : 7.465 86.866 2377 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.52 % Allowed : 17.26 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2023 helix: 1.36 (0.17), residues: 887 sheet: -0.90 (0.34), residues: 206 loop : -0.80 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 585 TYR 0.014 0.001 TYR B 554 PHE 0.010 0.001 PHE A 24 TRP 0.013 0.001 TRP B 437 HIS 0.008 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (16810) covalent geometry : angle 0.50239 / 0.26 (22713) hydrogen bonds : bond 0.03594 / 2.31 ( 777) hydrogen bonds : angle 4.73056 / 3.25 ( 2163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8593 (m-80) cc_final: 0.8207 (m-80) REVERT: A 437 GLU cc_start: 0.8539 (tt0) cc_final: 0.8314 (tt0) REVERT: A 591 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7318 (mp0) REVERT: B 289 MET cc_start: 0.8971 (mmm) cc_final: 0.8354 (mmm) REVERT: C 199 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6067 (mtt) REVERT: C 236 CYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8614 (m) REVERT: C 244 GLN cc_start: 0.7712 (tp40) cc_final: 0.7080 (tp40) REVERT: C 715 GLU cc_start: 0.7771 (pp20) cc_final: 0.7437 (pp20) REVERT: C 716 GLU cc_start: 0.7046 (pt0) cc_final: 0.6843 (pt0) outliers start: 27 outliers final: 21 residues processed: 272 average time/residue: 0.2825 time to fit residues: 119.1488 Evaluate side-chains 268 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101134 restraints weight = 99441.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105300 restraints weight = 36417.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107767 restraints weight = 20350.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109130 restraints weight = 14921.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109795 restraints weight = 12802.883| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16810 Z= 0.188 Angle : 0.529 6.292 22713 Z= 0.279 Chirality : 0.038 0.144 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.493 87.104 2377 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.63 % Allowed : 17.37 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2023 helix: 1.27 (0.17), residues: 888 sheet: -0.93 (0.34), residues: 206 loop : -0.87 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.017 0.001 TYR B 554 PHE 0.013 0.001 PHE A 24 TRP 0.016 0.001 TRP B 437 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (16810) covalent geometry : angle 0.52874 / 0.28 (22713) hydrogen bonds : bond 0.03755 / 2.40 ( 777) hydrogen bonds : angle 4.82535 / 3.31 ( 2163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8614 (m-80) cc_final: 0.8266 (m-80) REVERT: A 437 GLU cc_start: 0.8574 (tt0) cc_final: 0.8351 (tt0) REVERT: A 591 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7347 (mp0) REVERT: B 289 MET cc_start: 0.8999 (mmm) cc_final: 0.8336 (mmm) REVERT: C 199 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6124 (mtt) REVERT: C 236 CYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8676 (m) REVERT: C 454 GLU cc_start: 0.5190 (pt0) cc_final: 0.4882 (pm20) REVERT: C 716 GLU cc_start: 0.7046 (pt0) cc_final: 0.6844 (pt0) outliers start: 29 outliers final: 25 residues processed: 263 average time/residue: 0.2696 time to fit residues: 110.9156 Evaluate side-chains 270 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.136875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102113 restraints weight = 98878.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106350 restraints weight = 36122.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108827 restraints weight = 20148.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110183 restraints weight = 14782.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110748 restraints weight = 12681.991| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16810 Z= 0.126 Angle : 0.507 6.727 22713 Z= 0.265 Chirality : 0.038 0.148 2500 Planarity : 0.004 0.062 2871 Dihedral : 7.508 87.335 2377 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.52 % Allowed : 17.59 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2023 helix: 1.34 (0.17), residues: 884 sheet: -0.91 (0.34), residues: 206 loop : -0.80 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 585 TYR 0.014 0.001 TYR B 554 PHE 0.011 0.001 PHE A 24 TRP 0.015 0.001 TRP B 437 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16810) covalent geometry : angle 0.50733 / 0.27 (22713) hydrogen bonds : bond 0.03620 / 2.31 ( 777) hydrogen bonds : angle 4.73453 / 3.25 ( 2163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8615 (m-80) cc_final: 0.8260 (m-80) REVERT: A 437 GLU cc_start: 0.8544 (tt0) cc_final: 0.8328 (tt0) REVERT: A 591 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7302 (mp0) REVERT: B 289 MET cc_start: 0.9015 (mmm) cc_final: 0.8322 (mmm) REVERT: C 199 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.6131 (mtt) REVERT: C 236 CYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8679 (m) REVERT: C 244 GLN cc_start: 0.7719 (tp40) cc_final: 0.7081 (tp40) REVERT: C 454 GLU cc_start: 0.5172 (pt0) cc_final: 0.4837 (pm20) REVERT: C 715 GLU cc_start: 0.7760 (pp20) cc_final: 0.7399 (pp20) outliers start: 27 outliers final: 24 residues processed: 266 average time/residue: 0.2876 time to fit residues: 119.5918 Evaluate side-chains 272 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 162 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS B 276 ASN B 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099548 restraints weight = 99036.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103680 restraints weight = 36684.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106122 restraints weight = 20648.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107455 restraints weight = 15197.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107962 restraints weight = 13045.882| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16810 Z= 0.215 Angle : 0.556 7.588 22713 Z= 0.296 Chirality : 0.039 0.145 2500 Planarity : 0.004 0.060 2871 Dihedral : 7.592 88.418 2377 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.69 % Allowed : 17.54 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2023 helix: 1.13 (0.17), residues: 891 sheet: -0.94 (0.34), residues: 207 loop : -0.95 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 601 TYR 0.019 0.002 TYR B 554 PHE 0.014 0.002 PHE A 24 TRP 0.019 0.002 TRP B 437 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16810) covalent geometry : angle 0.55573 / 0.30 (22713) hydrogen bonds : bond 0.03867 / 2.47 ( 777) hydrogen bonds : angle 4.90143 / 3.36 ( 2163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8638 (m-80) cc_final: 0.8342 (m-80) REVERT: A 437 GLU cc_start: 0.8603 (tt0) cc_final: 0.8378 (tt0) REVERT: A 591 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7371 (mp0) REVERT: B 289 MET cc_start: 0.9012 (mmm) cc_final: 0.8301 (mmm) REVERT: C 53 MET cc_start: 0.6577 (mmm) cc_final: 0.6353 (mmt) REVERT: C 199 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6153 (mtt) REVERT: C 236 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8786 (m) REVERT: C 244 GLN cc_start: 0.7831 (tp40) cc_final: 0.7114 (tp40) outliers start: 30 outliers final: 26 residues processed: 263 average time/residue: 0.2875 time to fit residues: 118.4724 Evaluate side-chains 269 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 135 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 190 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100650 restraints weight = 99401.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104843 restraints weight = 36490.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107313 restraints weight = 20465.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108644 restraints weight = 15046.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109329 restraints weight = 12947.689| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16810 Z= 0.142 Angle : 0.519 7.059 22713 Z= 0.272 Chirality : 0.038 0.148 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.591 88.001 2377 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.52 % Allowed : 17.65 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2023 helix: 1.25 (0.17), residues: 885 sheet: -0.93 (0.34), residues: 207 loop : -0.86 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 601 TYR 0.016 0.001 TYR B 554 PHE 0.013 0.001 PHE A 24 TRP 0.018 0.001 TRP B 437 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16810) covalent geometry : angle 0.51884 / 0.27 (22713) hydrogen bonds : bond 0.03670 / 2.34 ( 777) hydrogen bonds : angle 4.78828 / 3.29 ( 2163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 125 is missing expected H atoms. Skipping. Residue LYS 138 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8600 (m-80) cc_final: 0.8333 (m-80) REVERT: A 437 GLU cc_start: 0.8602 (tt0) cc_final: 0.8362 (tt0) REVERT: A 591 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7308 (mp0) REVERT: B 289 MET cc_start: 0.8992 (mmm) cc_final: 0.8287 (mmm) REVERT: C 53 MET cc_start: 0.6541 (mmm) cc_final: 0.6341 (mmt) REVERT: C 199 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6143 (mtt) REVERT: C 236 CYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8752 (m) REVERT: C 715 GLU cc_start: 0.7637 (pp20) cc_final: 0.7424 (pp20) outliers start: 27 outliers final: 25 residues processed: 263 average time/residue: 0.2908 time to fit residues: 120.1694 Evaluate side-chains 267 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 689 CYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 113 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101296 restraints weight = 98479.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105493 restraints weight = 35939.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107959 restraints weight = 20047.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109307 restraints weight = 14697.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109802 restraints weight = 12605.629| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16810 Z= 0.120 Angle : 0.516 8.470 22713 Z= 0.268 Chirality : 0.038 0.149 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.564 88.052 2377 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.57 % Allowed : 17.82 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2023 helix: 1.35 (0.17), residues: 885 sheet: -0.94 (0.34), residues: 206 loop : -0.80 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 601 TYR 0.017 0.001 TYR A 131 PHE 0.010 0.001 PHE C 121 TRP 0.017 0.001 TRP B 437 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16810) covalent geometry : angle 0.51627 / 0.27 (22713) hydrogen bonds : bond 0.03534 / 2.27 ( 777) hydrogen bonds : angle 4.68083 / 3.21 ( 2163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5868.99 seconds wall clock time: 100 minutes 54.51 seconds (6054.51 seconds total)