Starting phenix.real_space_refine on Fri May 30 03:11:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn1_19383/05_2025/8rn1_19383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn1_19383/05_2025/8rn1_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_19383/05_2025/8rn1_19383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn1_19383/05_2025/8rn1_19383.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn1_19383/05_2025/8rn1_19383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn1_19383/05_2025/8rn1_19383.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.83, per 1000 atoms: 0.57 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: 9.59 Conformation dependent library (CDL) restraints added in 3.3 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: 2.80 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: 12.93 Time building geometry restraints manager: 11.12 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: 59782 1.97 - 3.95: 402 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=" N PRO B 509 " pdb=" CA PRO B 509 " pdb=" C PRO B 509 " ideal model delta sigma weight residual 111.13 114.95 -3.82 1.49e+00 4.50e-01 6.56e+00 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 114.56 111.33 3.23 1.27e+00 6.20e-01 6.49e+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: 1657 0.030 - 0.060: 607 0.060 - 0.089: 124 0.089 - 0.119: 93 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.540 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 71.730 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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= 0.127 Angle : 0.532 9.874 22713 Z= 0.285 Chirality : 0.037 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 : 10.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.017 0.001 TRP B 437 HIS 0.003 0.001 HIS C 184 PHE 0.015 0.001 PHE B 511 TYR 0.013 0.001 TYR B 554 ARG 0.003 0.000 ARG C 178 Details of bonding type rmsd hydrogen bonds : bond 0.14227 ( 777) hydrogen bonds : angle 6.09365 ( 2163) covalent geometry : bond 0.00275 (16810) covalent geometry : angle 0.53217 (22713) *********************** 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 : 2.444 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: 0.6297 time to fit residues: 262.5045 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 : 2.623 ------------------------------------------------------------------------------- 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 171 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105102 restraints weight = 98185.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109433 restraints weight = 35523.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111960 restraints weight = 19715.147| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16810 Z= 0.128 Angle : 0.533 7.190 22713 Z= 0.279 Chirality : 0.038 0.155 2500 Planarity : 0.004 0.075 2871 Dihedral : 7.489 85.472 2381 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.90 % Allowed : 18.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2023 helix: 1.40 (0.17), residues: 872 sheet: -0.61 (0.34), residues: 209 loop : -0.66 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 663 PHE 0.011 0.001 PHE A 36 TYR 0.013 0.001 TYR B 554 ARG 0.003 0.000 ARG B 666 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 777) hydrogen bonds : angle 5.06152 ( 2163) covalent geometry : bond 0.00284 (16810) covalent geometry : angle 0.53276 (22713) *********************** 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 282 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 2.841 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: A 642 MET cc_start: 0.8430 (mmt) cc_final: 0.8202 (mmp) REVERT: B 289 MET cc_start: 0.8885 (mmm) cc_final: 0.8582 (mmm) REVERT: B 601 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7918 (ptm-80) REVERT: C 183 ILE cc_start: 0.6956 (tt) cc_final: 0.6639 (mt) outliers start: 16 outliers final: 13 residues processed: 272 average time/residue: 0.6516 time to fit residues: 269.5734 Evaluate side-chains 259 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU 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 199 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 531 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN C 435 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099239 restraints weight = 99058.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103379 restraints weight = 36671.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105803 restraints weight = 20683.463| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16810 Z= 0.248 Angle : 0.587 6.908 22713 Z= 0.315 Chirality : 0.041 0.151 2500 Planarity : 0.004 0.068 2871 Dihedral : 7.657 87.574 2377 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.69 % Allowed : 17.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2023 helix: 1.02 (0.17), residues: 887 sheet: -0.87 (0.33), residues: 207 loop : -0.93 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 437 HIS 0.010 0.001 HIS A 99 PHE 0.020 0.002 PHE A 24 TYR 0.023 0.002 TYR B 554 ARG 0.004 0.001 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 777) hydrogen bonds : angle 5.19149 ( 2163) covalent geometry : bond 0.00551 (16810) covalent geometry : angle 0.58668 (22713) *********************** 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 285 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 2.719 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: 0.8626 (m-80) cc_final: 0.8255 (m-80) REVERT: A 507 LEU cc_start: 0.9091 (mt) cc_final: 0.8878 (mp) REVERT: A 591 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7506 (mp0) REVERT: B 276 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6173 (m110) REVERT: B 289 MET cc_start: 0.8901 (mmm) cc_final: 0.8372 (mmm) REVERT: C 183 ILE cc_start: 0.7019 (tt) cc_final: 0.6701 (mt) REVERT: C 199 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6002 (mtt) REVERT: C 724 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7461 (tm-30) outliers start: 30 outliers final: 21 residues processed: 272 average time/residue: 0.6372 time to fit residues: 264.7679 Evaluate side-chains 267 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 145 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 292 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 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 369 CYS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 701 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 141 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS B 265 ASN B 292 ASN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102187 restraints weight = 99240.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106415 restraints weight = 35932.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108904 restraints weight = 20029.840| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16810 Z= 0.118 Angle : 0.516 7.175 22713 Z= 0.268 Chirality : 0.038 0.151 2500 Planarity : 0.004 0.068 2871 Dihedral : 7.590 87.550 2377 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2023 helix: 1.27 (0.17), residues: 881 sheet: -0.86 (0.33), residues: 207 loop : -0.82 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.013 0.001 HIS C 184 PHE 0.012 0.001 PHE A 24 TYR 0.015 0.001 TYR B 554 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 777) hydrogen bonds : angle 4.83837 ( 2163) covalent geometry : bond 0.00267 (16810) covalent geometry : angle 0.51635 (22713) *********************** 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 294 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 2.796 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: A 36 PHE cc_start: 0.8671 (m-80) cc_final: 0.8333 (m-80) REVERT: A 184 LYS cc_start: 0.7318 (ptmt) cc_final: 0.6932 (tptp) REVERT: A 437 GLU cc_start: 0.8562 (tt0) cc_final: 0.8284 (tt0) REVERT: A 591 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7331 (mp0) REVERT: B 289 MET cc_start: 0.8984 (mmm) cc_final: 0.8308 (mmm) REVERT: C 199 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6041 (mtt) REVERT: C 236 CYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8590 (m) REVERT: C 508 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7808 (ptp90) outliers start: 28 outliers final: 18 residues processed: 281 average time/residue: 0.6328 time to fit residues: 272.2000 Evaluate side-chains 272 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 107 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 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 449 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 276 ASN B 292 ASN C 241 ASN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101569 restraints weight = 99001.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105776 restraints weight = 36029.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108220 restraints weight = 20042.200| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 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 = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16810 Z= 0.153 Angle : 0.519 5.847 22713 Z= 0.273 Chirality : 0.038 0.147 2500 Planarity : 0.004 0.063 2871 Dihedral : 7.579 89.065 2377 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2023 helix: 1.31 (0.17), residues: 885 sheet: -0.86 (0.34), residues: 207 loop : -0.85 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.011 0.001 HIS C 184 PHE 0.012 0.001 PHE A 24 TYR 0.016 0.001 TYR B 554 ARG 0.003 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 777) hydrogen bonds : angle 4.80087 ( 2163) covalent geometry : bond 0.00343 (16810) covalent geometry : angle 0.51914 (22713) *********************** 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 273 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 2.457 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: 0.8662 (m-80) cc_final: 0.8353 (m-80) REVERT: A 184 LYS cc_start: 0.7237 (ptmt) cc_final: 0.6887 (tptp) REVERT: A 437 GLU cc_start: 0.8574 (tt0) cc_final: 0.8340 (tt0) REVERT: A 591 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7348 (mp0) REVERT: A 621 GLU cc_start: 0.7353 (tp30) cc_final: 0.7146 (tp30) REVERT: B 289 MET cc_start: 0.8984 (mmm) cc_final: 0.8297 (mmm) REVERT: C 184 HIS cc_start: 0.7241 (m-70) cc_final: 0.7040 (m-70) REVERT: C 199 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6038 (mtt) REVERT: C 508 ARG cc_start: 0.8202 (ptp-110) cc_final: 0.7223 (mtt90) outliers start: 27 outliers final: 23 residues processed: 262 average time/residue: 0.6435 time to fit residues: 258.8125 Evaluate side-chains 269 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 ASP 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 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 330 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 561 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 24 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103058 restraints weight = 99199.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107269 restraints weight = 35842.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109743 restraints weight = 19904.614| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.107 | | 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) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16810 Z= 0.110 Angle : 0.497 5.612 22713 Z= 0.257 Chirality : 0.038 0.143 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.529 88.619 2377 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.80 % Allowed : 17.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2023 helix: 1.44 (0.17), residues: 886 sheet: -0.90 (0.34), residues: 206 loop : -0.81 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 437 HIS 0.008 0.001 HIS C 184 PHE 0.010 0.001 PHE A 24 TYR 0.014 0.001 TYR B 554 ARG 0.004 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 777) hydrogen bonds : angle 4.61925 ( 2163) covalent geometry : bond 0.00251 (16810) covalent geometry : angle 0.49716 (22713) *********************** 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 292 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 2.589 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: 0.8647 (m-80) cc_final: 0.8392 (m-80) REVERT: A 184 LYS cc_start: 0.7148 (ptmt) cc_final: 0.6822 (tptp) REVERT: A 437 GLU cc_start: 0.8574 (tt0) cc_final: 0.8359 (tt0) REVERT: A 591 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7262 (mp0) REVERT: A 621 GLU cc_start: 0.7378 (tp30) cc_final: 0.7155 (tp30) REVERT: B 289 MET cc_start: 0.9010 (mmm) cc_final: 0.8301 (mmm) REVERT: C 199 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6001 (mtt) REVERT: C 236 CYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8621 (m) REVERT: C 508 ARG cc_start: 0.8196 (ptp-110) cc_final: 0.7302 (mtt90) REVERT: C 572 MET cc_start: 0.7560 (pmm) cc_final: 0.7313 (pmm) REVERT: C 715 GLU cc_start: 0.7756 (pp20) cc_final: 0.7396 (pp20) outliers start: 32 outliers final: 22 residues processed: 280 average time/residue: 0.6404 time to fit residues: 273.6169 Evaluate side-chains 275 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 476 MET 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 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 39 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 chunk 50 optimal weight: 0.2980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102492 restraints weight = 98834.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106659 restraints weight = 36010.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109127 restraints weight = 20056.877| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 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 = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16810 Z= 0.107 Angle : 0.494 5.857 22713 Z= 0.256 Chirality : 0.037 0.143 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.503 89.019 2377 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2023 helix: 1.51 (0.17), residues: 887 sheet: -0.91 (0.33), residues: 206 loop : -0.75 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 100 HIS 0.001 0.000 HIS B 32 PHE 0.011 0.001 PHE B 511 TYR 0.012 0.001 TYR B 554 ARG 0.007 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 777) hydrogen bonds : angle 4.53468 ( 2163) covalent geometry : bond 0.00245 (16810) covalent geometry : angle 0.49383 (22713) *********************** 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 282 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 2.617 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: 0.8594 (m-80) cc_final: 0.8353 (m-80) REVERT: A 184 LYS cc_start: 0.7129 (ptmt) cc_final: 0.6820 (tptp) REVERT: A 591 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7305 (mp0) REVERT: B 289 MET cc_start: 0.9005 (mmm) cc_final: 0.8225 (mmm) REVERT: C 199 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5971 (mtt) REVERT: C 236 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8668 (m) REVERT: C 417 ARG cc_start: 0.6679 (mmp-170) cc_final: 0.6459 (mmm160) REVERT: C 454 GLU cc_start: 0.5557 (pt0) cc_final: 0.4954 (pm20) REVERT: C 508 ARG cc_start: 0.8162 (ptp-110) cc_final: 0.7282 (mtt90) REVERT: C 572 MET cc_start: 0.7622 (pmm) cc_final: 0.7358 (pmm) outliers start: 27 outliers final: 19 residues processed: 272 average time/residue: 0.6415 time to fit residues: 263.1816 Evaluate side-chains 268 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 2.542 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 103 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 643 HIS B 265 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100635 restraints weight = 99846.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104772 restraints weight = 36380.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107211 restraints weight = 20284.422| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16810 Z= 0.183 Angle : 0.525 6.117 22713 Z= 0.277 Chirality : 0.039 0.165 2500 Planarity : 0.004 0.061 2871 Dihedral : 7.583 88.990 2377 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.97 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2023 helix: 1.38 (0.17), residues: 893 sheet: -1.02 (0.34), residues: 199 loop : -0.86 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.010 0.001 HIS C 184 PHE 0.012 0.001 PHE A 24 TYR 0.017 0.001 TYR B 554 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 777) hydrogen bonds : angle 4.67910 ( 2163) covalent geometry : bond 0.00410 (16810) covalent geometry : angle 0.52506 (22713) *********************** 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 285 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.765 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: 0.8661 (m-80) cc_final: 0.8432 (m-80) REVERT: A 184 LYS cc_start: 0.7210 (ptmt) cc_final: 0.6880 (tptp) REVERT: B 289 MET cc_start: 0.9076 (mmm) cc_final: 0.8210 (mmm) REVERT: C 53 MET cc_start: 0.6652 (mmm) cc_final: 0.6313 (mmp) REVERT: C 184 HIS cc_start: 0.7025 (m-70) cc_final: 0.6799 (m90) REVERT: C 236 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8680 (m) REVERT: C 508 ARG cc_start: 0.8192 (ptp-110) cc_final: 0.7333 (mtt90) REVERT: C 572 MET cc_start: 0.7648 (pmm) cc_final: 0.7346 (pmm) REVERT: C 716 GLU cc_start: 0.6691 (pt0) cc_final: 0.6443 (pt0) outliers start: 35 outliers final: 29 residues processed: 274 average time/residue: 0.6272 time to fit residues: 260.5809 Evaluate side-chains 276 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 153 ASN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 328 ASP 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 156 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 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 79 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102068 restraints weight = 99315.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106271 restraints weight = 35923.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108744 restraints weight = 19944.211| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2233 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= 0.116 Angle : 0.505 7.341 22713 Z= 0.262 Chirality : 0.038 0.142 2500 Planarity : 0.004 0.065 2871 Dihedral : 7.545 88.785 2377 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.63 % Allowed : 17.71 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2023 helix: 1.47 (0.17), residues: 893 sheet: -1.05 (0.34), residues: 198 loop : -0.79 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.008 0.001 HIS C 184 PHE 0.011 0.001 PHE A 24 TYR 0.014 0.001 TYR B 554 ARG 0.007 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 777) hydrogen bonds : angle 4.50590 ( 2163) covalent geometry : bond 0.00267 (16810) covalent geometry : angle 0.50508 (22713) *********************** 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 278 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 2.463 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: A 23 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 184 LYS cc_start: 0.7134 (ptmt) cc_final: 0.6838 (tptp) REVERT: B 289 MET cc_start: 0.9072 (mmm) cc_final: 0.8170 (mmm) REVERT: C 53 MET cc_start: 0.6593 (mmm) cc_final: 0.6276 (mmp) REVERT: C 184 HIS cc_start: 0.7016 (m-70) cc_final: 0.6807 (m90) REVERT: C 236 CYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8645 (m) REVERT: C 508 ARG cc_start: 0.8172 (ptp-110) cc_final: 0.7327 (mtt90) REVERT: C 572 MET cc_start: 0.7642 (pmm) cc_final: 0.7370 (pmm) REVERT: C 610 MET cc_start: 0.7079 (tpt) cc_final: 0.6698 (tpt) outliers start: 29 outliers final: 25 residues processed: 268 average time/residue: 0.6297 time to fit residues: 258.4706 Evaluate side-chains 270 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 437 GLU 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 248 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 156 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 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 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 2 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 475 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102672 restraints weight = 98463.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106901 restraints weight = 35859.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109379 restraints weight = 19929.616| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 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 = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16810 Z= 0.100 Angle : 0.502 7.351 22713 Z= 0.258 Chirality : 0.038 0.166 2500 Planarity : 0.004 0.064 2871 Dihedral : 7.502 88.847 2377 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.57 % Allowed : 17.88 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2023 helix: 1.59 (0.17), residues: 893 sheet: -0.96 (0.34), residues: 199 loop : -0.71 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 437 HIS 0.008 0.001 HIS C 184 PHE 0.011 0.001 PHE A 36 TYR 0.020 0.001 TYR C 117 ARG 0.008 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 777) hydrogen bonds : angle 4.38879 ( 2163) covalent geometry : bond 0.00230 (16810) covalent geometry : angle 0.50236 (22713) ********************** 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 282 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 2.669 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: A 23 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 184 LYS cc_start: 0.7055 (ptmt) cc_final: 0.6751 (tptp) REVERT: B 289 MET cc_start: 0.9082 (mmm) cc_final: 0.8135 (mmm) REVERT: C 53 MET cc_start: 0.6520 (mmm) cc_final: 0.6199 (mmp) REVERT: C 236 CYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (m) REVERT: C 419 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: C 508 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7325 (mtt90) REVERT: C 572 MET cc_start: 0.7592 (pmm) cc_final: 0.7331 (pmm) REVERT: C 610 MET cc_start: 0.7019 (tpt) cc_final: 0.6623 (tpt) outliers start: 28 outliers final: 24 residues processed: 273 average time/residue: 0.6310 time to fit residues: 261.1369 Evaluate side-chains 270 residues out of total 1778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 437 GLU 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 248 ILE Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 156 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 236 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 419 GLU 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 43 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3893 r_free = 0.3893 target = 0.135201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101843 restraints weight = 98659.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105978 restraints weight = 36033.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108399 restraints weight = 20154.640| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2424 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= 0.117 Angle : 0.503 8.892 22713 Z= 0.260 Chirality : 0.038 0.142 2500 Planarity : 0.004 0.065 2871 Dihedral : 7.501 88.879 2377 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.63 % Allowed : 17.82 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2023 helix: 1.57 (0.17), residues: 893 sheet: -0.91 (0.35), residues: 199 loop : -0.73 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 337 HIS 0.002 0.000 HIS C 184 PHE 0.012 0.001 PHE A 24 TYR 0.016 0.001 TYR C 117 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 777) hydrogen bonds : angle 4.40273 ( 2163) covalent geometry : bond 0.00268 (16810) covalent geometry : angle 0.50337 (22713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11071.19 seconds wall clock time: 191 minutes 56.06 seconds (11516.06 seconds total)