Starting phenix.real_space_refine on Fri Jul 3 06:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.map" model { file = "/net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o58_70127/07_2026/9o58_70127.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 Ca 1 9.91 5 Zn 1 6.06 5 S 84 5.16 5 C 7858 2.51 5 N 2100 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12422 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5082 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3941 Classifications: {'peptide': 490} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 466} Chain: "C" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1646 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 85 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1296 SG CYS A 184 42.422 79.198 118.240 1.00134.71 S Time building chain proxies: 2.28, per 1000 atoms: 0.18 Number of scatterers: 12422 At special positions: 0 Unit cell: (105.216, 115.08, 207.966, 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) Zn 1 29.99 Ca 1 19.99 S 84 16.00 O 2378 8.00 N 2100 7.00 C 7858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 453 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 593 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 616 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 838 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 901 " - " ASN A 498 " " NAG A 902 " - " ASN A 551 " " NAG A 903 " - " ASN A 157 " " NAG A 904 " - " ASN A 264 " " NAG A 905 " - " ASN A 452 " " NAG A 906 " - " ASN A 594 " " NAG E 1 " - " ASN A 539 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 408.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 908 " pdb="ZN ZN A 908 " - pdb=" NE2 HIS A 409 " pdb="ZN ZN A 908 " - pdb=" NE2 HIS A 405 " pdb="ZN ZN A 908 " - pdb=" ND1 HIS A 415 " pdb="ZN ZN A 908 " - pdb=" SG CYS A 184 " Number of angles added : 1 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2918 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 20 sheets defined 28.1% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.656A pdb=" N SER A 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.736A pdb=" N PHE A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 175 through 180 removed outlier: 4.035A pdb=" N GLN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 265 removed outlier: 3.539A pdb=" N GLU A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.536A pdb=" N LEU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.788A pdb=" N GLY A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.954A pdb=" N LYS A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.593A pdb=" N THR A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 647 through 659 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.617A pdb=" N GLY A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 697 removed outlier: 4.285A pdb=" N LEU A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 678 " --> pdb=" O GLY A 674 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'B' and resid 372 through 378 removed outlier: 3.502A pdb=" N TRP B 377 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.534A pdb=" N ILE B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 480 through 496 removed outlier: 4.046A pdb=" N ASP B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 516 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 612 through 619 removed outlier: 3.777A pdb=" N MET B 619 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 633 removed outlier: 3.570A pdb=" N GLN B 632 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 633 " --> pdb=" O CYS B 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 629 through 633' Processing helix chain 'B' and resid 634 through 641 removed outlier: 4.250A pdb=" N LYS B 638 " --> pdb=" O HIS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 666 through 689 removed outlier: 3.548A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 687 " --> pdb=" O ASP B 683 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 688 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 712 removed outlier: 5.769A pdb=" N ILE B 695 " --> pdb=" O HIS B 691 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 738 removed outlier: 3.657A pdb=" N PHE B 725 " --> pdb=" O ALA B 721 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 763 removed outlier: 3.699A pdb=" N ILE B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 788 removed outlier: 3.814A pdb=" N PHE B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA B 786 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 788 " --> pdb=" O ALA B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 825 removed outlier: 3.513A pdb=" N ARG B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 806 " --> pdb=" O ARG B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 832 No H-bonds generated for 'chain 'B' and resid 830 through 832' Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.809A pdb=" N THR B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.699A pdb=" N LYS D 65 " --> pdb=" O THR D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.859A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.650A pdb=" N LEU D 195 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.502A pdb=" N LEU A 45 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 116 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.419A pdb=" N VAL A 96 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 225 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 280 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A 227 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 282 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 229 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A 284 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 231 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU A 334 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 226 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS A 336 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 228 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 338 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 230 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 removed outlier: 3.648A pdb=" N TYR A 369 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'A' and resid 522 through 523 removed outlier: 3.553A pdb=" N LYS A 523 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.617A pdb=" N ILE A 579 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA8, first strand: chain 'B' and resid 432 through 440 removed outlier: 3.539A pdb=" N THR B 435 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 511 removed outlier: 3.514A pdb=" N ILE B 509 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 500 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 511 " --> pdb=" O GLY B 498 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 499 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 556 through 558 removed outlier: 3.802A pdb=" N GLU B 579 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 610 through 611 removed outlier: 4.072A pdb=" N CYS B 601 " --> pdb=" O TYR B 622 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 622 " --> pdb=" O CYS B 601 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.612A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 117 removed outlier: 5.785A pdb=" N LEU C 135 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER C 177 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN C 137 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 175 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.512A pdb=" N GLN C 147 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 149 through 150 removed outlier: 4.066A pdb=" N VAL C 150 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.514A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.661A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.661A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG D 98 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 126 through 129 378 hydrogen bonds defined for protein. 999 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: 1.66 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4016 1.34 - 1.47: 3110 1.47 - 1.59: 5483 1.59 - 1.72: 0 1.72 - 1.84: 103 Bond restraints: 12712 Sorted by residual: bond pdb=" CG PRO C 120 " pdb=" CD PRO C 120 " ideal model delta sigma weight residual 1.503 1.247 0.256 3.40e-02 8.65e+02 5.66e+01 bond pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 1.527 1.501 0.026 1.37e-02 5.33e+03 3.70e+00 bond pdb=" CA ASN A 475 " pdb=" C ASN A 475 " ideal model delta sigma weight residual 1.522 1.500 0.023 1.19e-02 7.06e+03 3.67e+00 bond pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.45e+00 bond pdb=" CA LYS A 476 " pdb=" C LYS A 476 " ideal model delta sigma weight residual 1.523 1.500 0.024 1.32e-02 5.74e+03 3.24e+00 ... (remaining 12707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 17169 3.93 - 7.86: 54 7.86 - 11.79: 10 11.79 - 15.71: 0 15.71 - 19.64: 2 Bond angle restraints: 17235 Sorted by residual: angle pdb=" N PRO C 120 " pdb=" CD PRO C 120 " pdb=" CG PRO C 120 " ideal model delta sigma weight residual 103.20 83.63 19.57 1.50e+00 4.44e-01 1.70e+02 angle pdb=" CA PRO C 120 " pdb=" CB PRO C 120 " pdb=" CG PRO C 120 " ideal model delta sigma weight residual 104.50 84.86 19.64 1.90e+00 2.77e-01 1.07e+02 angle pdb=" C ASN A 452 " pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " ideal model delta sigma weight residual 111.22 100.75 10.47 1.24e+00 6.50e-01 7.13e+01 angle pdb=" N PRO C 120 " pdb=" CA PRO C 120 " pdb=" CB PRO C 120 " ideal model delta sigma weight residual 103.25 96.26 6.99 1.05e+00 9.07e-01 4.43e+01 angle pdb=" CA PRO C 120 " pdb=" N PRO C 120 " pdb=" CD PRO C 120 " ideal model delta sigma weight residual 112.00 103.45 8.55 1.40e+00 5.10e-01 3.73e+01 ... (remaining 17230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6539 17.94 - 35.88: 934 35.88 - 53.82: 227 53.82 - 71.75: 46 71.75 - 89.69: 16 Dihedral angle restraints: 7762 sinusoidal: 3221 harmonic: 4541 Sorted by residual: dihedral pdb=" CB CYS A 521 " pdb=" SG CYS A 521 " pdb=" SG CYS A 548 " pdb=" CB CYS A 548 " ideal model delta sinusoidal sigma weight residual -86.00 -168.14 82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual 93.00 174.61 -81.61 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS B 838 " pdb=" SG CYS B 838 " pdb=" SG CYS B 846 " pdb=" CB CYS B 846 " ideal model delta sinusoidal sigma weight residual 93.00 169.79 -76.79 1 1.00e+01 1.00e-02 7.41e+01 ... (remaining 7759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1907 0.136 - 0.271: 8 0.271 - 0.407: 3 0.407 - 0.543: 0 0.543 - 0.678: 1 Chirality restraints: 1919 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 452 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN A 594 " pdb=" N ASN A 594 " pdb=" C ASN A 594 " pdb=" CB ASN A 594 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1916 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 452 " 0.078 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" CG ASN A 452 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A 452 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 452 " -0.072 2.00e-02 2.50e+03 pdb=" C1 NAG A 905 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 594 " -0.002 2.00e-02 2.50e+03 5.88e-02 4.33e+01 pdb=" CG ASN A 594 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 594 " 0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 594 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG A 906 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " 0.022 2.00e-02 2.50e+03 2.55e-02 1.63e+01 pdb=" CG TRP D 47 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " -0.000 2.00e-02 2.50e+03 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 52 2.42 - 3.04: 7634 3.04 - 3.66: 18843 3.66 - 4.28: 26573 4.28 - 4.90: 43835 Nonbonded interactions: 96937 Sorted by model distance: nonbonded pdb=" OE1 GLN A 278 " pdb=" NH1 ARG A 473 " model vdw 1.798 3.120 nonbonded pdb=" N GLU A 472 " pdb=" OE1 GLU A 472 " model vdw 2.173 3.120 nonbonded pdb=" O TYR B 369 " pdb=" OH TYR B 382 " model vdw 2.184 3.040 nonbonded pdb=" OG SER D 30 " pdb=" OD1 ASN D 74 " model vdw 2.184 3.040 nonbonded pdb=" N GLU D 105 " pdb=" OE1 GLU D 105 " model vdw 2.198 3.120 ... (remaining 96932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.256 12752 Z= 0.172 Angle : 0.777 19.643 17316 Z= 0.395 Chirality : 0.047 0.678 1919 Planarity : 0.004 0.076 2207 Dihedral : 17.255 89.693 4760 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.44 % Allowed : 29.54 % Favored : 70.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1557 helix: -0.37 (0.27), residues: 347 sheet: -0.03 (0.33), residues: 254 loop : -1.05 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 844 TYR 0.015 0.001 TYR A 352 PHE 0.030 0.001 PHE A 664 TRP 0.065 0.002 TRP D 47 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12712) covalent geometry : angle 0.69781 / 0.38 (17235) SS BOND : bond 0.00194 / 0.13 ( 28) SS BOND : angle 1.20176 / 0.81 ( 56) hydrogen bonds : bond 0.27847 / 18.64 ( 374) hydrogen bonds : angle 8.81458 / 6.12 ( 999) metal coordination : bond 0.01192 / 0.60 ( 4) metal coordination : angle 2.15584 / 1.54 ( 1) link_BETA1-4 : bond 0.00713 / 0.48 ( 1) link_BETA1-4 : angle 1.00292 / 0.61 ( 3) link_NAG-ASN : bond 0.00748 / 0.37 ( 7) link_NAG-ASN : angle 9.71036 / 8.42 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.400 Fit side-chains REVERT: B 801 LYS cc_start: 0.8497 (mmtt) cc_final: 0.7896 (mmtp) outliers start: 6 outliers final: 3 residues processed: 131 average time/residue: 0.0775 time to fit residues: 16.2422 Evaluate side-chains 117 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 832 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 233 HIS A 299 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN A 518 ASN A 535 GLN A 560 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 376 ASN B 391 GLN B 400 HIS B 468 HIS B 503 ASN B 510 GLN B 565 HIS B 632 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 158 ASN C 198 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 170 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.114519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085773 restraints weight = 30394.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088087 restraints weight = 15337.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088959 restraints weight = 10261.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089219 restraints weight = 8918.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089341 restraints weight = 8480.336| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12752 Z= 0.178 Angle : 0.642 9.671 17316 Z= 0.330 Chirality : 0.044 0.227 1919 Planarity : 0.004 0.046 2207 Dihedral : 5.694 54.914 1865 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.64 % Allowed : 24.82 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1557 helix: 0.10 (0.27), residues: 362 sheet: -0.13 (0.31), residues: 277 loop : -1.10 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.025 0.002 TYR C 49 PHE 0.019 0.002 PHE A 664 TRP 0.032 0.001 TRP D 47 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (12712) covalent geometry : angle 0.62321 / 0.33 (17235) SS BOND : bond 0.00366 / 0.27 ( 28) SS BOND : angle 1.06516 / 0.75 ( 56) hydrogen bonds : bond 0.05199 / 3.41 ( 374) hydrogen bonds : angle 6.20231 / 4.24 ( 999) metal coordination : bond 0.01952 / 0.94 ( 4) metal coordination : angle 4.49941 / 3.21 ( 1) link_BETA1-4 : bond 0.00280 / 0.19 ( 1) link_BETA1-4 : angle 0.82355 / 0.61 ( 3) link_NAG-ASN : bond 0.00729 / 0.39 ( 7) link_NAG-ASN : angle 4.14276 / 3.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7961 (mmm) cc_final: 0.7491 (mmp) REVERT: A 498 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.7036 (m-40) REVERT: A 535 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7564 (mm-40) REVERT: B 485 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: D 39 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7422 (tp-100) REVERT: D 57 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7214 (mmt) REVERT: D 73 ASP cc_start: 0.7873 (t0) cc_final: 0.7666 (t0) outliers start: 64 outliers final: 31 residues processed: 173 average time/residue: 0.0690 time to fit residues: 19.1998 Evaluate side-chains 144 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 560 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 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 = 0.3838 r_free = 0.3838 target = 0.115857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087123 restraints weight = 30728.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090446 restraints weight = 15569.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090354 restraints weight = 10227.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090715 restraints weight = 9109.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090721 restraints weight = 8510.245| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12752 Z= 0.121 Angle : 0.584 9.785 17316 Z= 0.294 Chirality : 0.042 0.236 1919 Planarity : 0.004 0.045 2207 Dihedral : 5.391 54.419 1861 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.64 % Allowed : 25.04 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1557 helix: 0.57 (0.28), residues: 351 sheet: -0.15 (0.31), residues: 277 loop : -1.06 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 844 TYR 0.023 0.001 TYR C 49 PHE 0.017 0.001 PHE B 749 TRP 0.016 0.001 TRP B 832 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12712) covalent geometry : angle 0.56773 / 0.29 (17235) SS BOND : bond 0.00268 / 0.21 ( 28) SS BOND : angle 0.93140 / 0.69 ( 56) hydrogen bonds : bond 0.04581 / 3.00 ( 374) hydrogen bonds : angle 5.76768 / 3.95 ( 999) metal coordination : bond 0.01281 / 0.66 ( 4) metal coordination : angle 1.98842 / 1.42 ( 1) link_BETA1-4 : bond 0.00359 / 0.24 ( 1) link_BETA1-4 : angle 0.78262 / 0.59 ( 3) link_NAG-ASN : bond 0.00418 / 0.27 ( 7) link_NAG-ASN : angle 3.78603 / 2.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8506 (mmt) cc_final: 0.8306 (mmt) REVERT: B 485 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: B 685 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: D 47 TRP cc_start: 0.8111 (t60) cc_final: 0.7829 (t60) outliers start: 64 outliers final: 37 residues processed: 180 average time/residue: 0.0741 time to fit residues: 21.5028 Evaluate side-chains 149 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 524 ASN A 535 GLN A 560 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 510 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN D 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.115219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086313 restraints weight = 30561.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089867 restraints weight = 15142.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089516 restraints weight = 9990.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089899 restraints weight = 9058.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089974 restraints weight = 8390.069| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12752 Z= 0.140 Angle : 0.583 9.092 17316 Z= 0.294 Chirality : 0.043 0.240 1919 Planarity : 0.004 0.045 2207 Dihedral : 5.282 54.641 1861 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.22 % Allowed : 25.47 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1557 helix: 0.69 (0.28), residues: 353 sheet: -0.21 (0.31), residues: 285 loop : -1.02 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 401 TYR 0.025 0.001 TYR C 49 PHE 0.013 0.001 PHE B 749 TRP 0.016 0.001 TRP B 832 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12712) covalent geometry : angle 0.56734 / 0.29 (17235) SS BOND : bond 0.00232 / 0.17 ( 28) SS BOND : angle 1.07425 / 0.75 ( 56) hydrogen bonds : bond 0.04128 / 2.69 ( 374) hydrogen bonds : angle 5.50239 / 3.77 ( 999) metal coordination : bond 0.01469 / 0.71 ( 4) metal coordination : angle 3.56223 / 2.54 ( 1) link_BETA1-4 : bond 0.00501 / 0.33 ( 1) link_BETA1-4 : angle 0.80582 / 0.58 ( 3) link_NAG-ASN : bond 0.00427 / 0.28 ( 7) link_NAG-ASN : angle 3.46959 / 2.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8520 (mmt) cc_final: 0.8313 (mmt) REVERT: A 498 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.7028 (m-40) REVERT: B 485 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: B 594 GLU cc_start: 0.7734 (pp20) cc_final: 0.7524 (pp20) REVERT: B 685 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: B 845 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7363 (p90) REVERT: C 61 ARG cc_start: 0.8952 (ptp-170) cc_final: 0.8712 (ptp-170) REVERT: C 189 HIS cc_start: 0.5462 (OUTLIER) cc_final: 0.5179 (t70) REVERT: D 47 TRP cc_start: 0.8177 (t60) cc_final: 0.7888 (t60) outliers start: 72 outliers final: 39 residues processed: 184 average time/residue: 0.0790 time to fit residues: 22.9937 Evaluate side-chains 159 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** D 39 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 = 0.3780 r_free = 0.3780 target = 0.112070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083037 restraints weight = 30925.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086032 restraints weight = 16170.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086443 restraints weight = 10444.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086836 restraints weight = 9770.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086750 restraints weight = 8458.504| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12752 Z= 0.261 Angle : 0.662 9.808 17316 Z= 0.335 Chirality : 0.045 0.232 1919 Planarity : 0.004 0.044 2207 Dihedral : 5.472 59.201 1861 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.88 % Allowed : 24.75 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1557 helix: 0.74 (0.29), residues: 345 sheet: -0.42 (0.30), residues: 287 loop : -1.12 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 401 TYR 0.026 0.002 TYR C 49 PHE 0.021 0.002 PHE B 841 TRP 0.019 0.001 TRP B 832 HIS 0.006 0.001 HIS B 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (12712) covalent geometry : angle 0.64618 / 0.33 (17235) SS BOND : bond 0.00401 / 0.30 ( 28) SS BOND : angle 1.41714 / 1.02 ( 56) hydrogen bonds : bond 0.04404 / 2.89 ( 374) hydrogen bonds : angle 5.42952 / 3.72 ( 999) metal coordination : bond 0.02646 / 1.30 ( 4) metal coordination : angle 6.53841 / 4.67 ( 1) link_BETA1-4 : bond 0.00177 / 0.12 ( 1) link_BETA1-4 : angle 0.91683 / 0.58 ( 3) link_NAG-ASN : bond 0.00426 / 0.29 ( 7) link_NAG-ASN : angle 3.33099 / 2.65 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 122 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8703 (tt) REVERT: A 498 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7140 (m-40) REVERT: B 397 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 485 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: B 594 GLU cc_start: 0.7909 (pp20) cc_final: 0.7663 (pp20) REVERT: B 685 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: B 845 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (p90) REVERT: C 61 ARG cc_start: 0.8995 (ptp-170) cc_final: 0.8640 (ptp-170) REVERT: C 189 HIS cc_start: 0.5423 (OUTLIER) cc_final: 0.5092 (t70) REVERT: D 39 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7254 (tp-100) REVERT: D 47 TRP cc_start: 0.8340 (t60) cc_final: 0.7961 (t60) REVERT: D 57 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: D 73 ASP cc_start: 0.7917 (t0) cc_final: 0.7680 (t0) outliers start: 81 outliers final: 52 residues processed: 188 average time/residue: 0.0757 time to fit residues: 22.6019 Evaluate side-chains 175 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 114 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.121836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.090511 restraints weight = 31577.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093445 restraints weight = 14788.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095285 restraints weight = 9666.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096377 restraints weight = 7552.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096979 restraints weight = 6558.370| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12752 Z= 0.205 Angle : 0.627 9.370 17316 Z= 0.317 Chirality : 0.044 0.220 1919 Planarity : 0.004 0.044 2207 Dihedral : 5.340 58.551 1861 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.39 % Allowed : 25.33 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1557 helix: 0.87 (0.29), residues: 344 sheet: -0.38 (0.31), residues: 279 loop : -1.11 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 401 TYR 0.027 0.001 TYR C 49 PHE 0.017 0.001 PHE B 841 TRP 0.020 0.001 TRP B 832 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (12712) covalent geometry : angle 0.61428 / 0.31 (17235) SS BOND : bond 0.00352 / 0.26 ( 28) SS BOND : angle 1.30348 / 0.94 ( 56) hydrogen bonds : bond 0.04038 / 2.63 ( 374) hydrogen bonds : angle 5.29428 / 3.62 ( 999) metal coordination : bond 0.02323 / 1.12 ( 4) metal coordination : angle 4.63063 / 3.31 ( 1) link_BETA1-4 : bond 0.00243 / 0.16 ( 1) link_BETA1-4 : angle 0.83613 / 0.57 ( 3) link_NAG-ASN : bond 0.00410 / 0.28 ( 7) link_NAG-ASN : angle 3.04497 / 2.46 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 126 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 241 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8260 (ttp-170) REVERT: A 411 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8530 (t80) REVERT: A 498 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.7151 (m-40) REVERT: B 397 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 484 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 485 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: B 594 GLU cc_start: 0.7959 (pp20) cc_final: 0.7697 (pp20) REVERT: B 685 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: B 845 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7573 (p90) REVERT: C 142 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7514 (mtt180) REVERT: C 189 HIS cc_start: 0.5508 (OUTLIER) cc_final: 0.5259 (t70) REVERT: D 39 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7287 (tp-100) REVERT: D 47 TRP cc_start: 0.8308 (t60) cc_final: 0.7886 (t60) REVERT: D 57 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7356 (mmt) REVERT: D 73 ASP cc_start: 0.7937 (t0) cc_final: 0.7604 (t0) REVERT: D 98 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7259 (tmm160) outliers start: 88 outliers final: 54 residues processed: 198 average time/residue: 0.0871 time to fit residues: 26.0911 Evaluate side-chains 185 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 790 TYR Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** D 39 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 = 0.3820 r_free = 0.3820 target = 0.114788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085021 restraints weight = 30354.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087631 restraints weight = 15636.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089271 restraints weight = 10620.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090261 restraints weight = 8476.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090714 restraints weight = 7427.122| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12752 Z= 0.124 Angle : 0.617 15.770 17316 Z= 0.309 Chirality : 0.043 0.249 1919 Planarity : 0.004 0.113 2207 Dihedral : 5.105 59.127 1861 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.86 % Allowed : 26.71 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1557 helix: 1.06 (0.29), residues: 342 sheet: -0.35 (0.31), residues: 279 loop : -1.07 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.029 0.001 TYR C 49 PHE 0.011 0.001 PHE B 812 TRP 0.020 0.001 TRP B 832 HIS 0.009 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (12712) covalent geometry : angle 0.59655 / 0.30 (17235) SS BOND : bond 0.00206 / 0.15 ( 28) SS BOND : angle 2.31679 / 1.78 ( 56) hydrogen bonds : bond 0.03696 / 2.42 ( 374) hydrogen bonds : angle 5.15757 / 3.53 ( 999) metal coordination : bond 0.01630 / 0.87 ( 4) metal coordination : angle 1.35895 / 0.97 ( 1) link_BETA1-4 : bond 0.00338 / 0.23 ( 1) link_BETA1-4 : angle 0.77125 / 0.59 ( 3) link_NAG-ASN : bond 0.00364 / 0.25 ( 7) link_NAG-ASN : angle 2.71979 / 2.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7083 (m-40) REVERT: A 515 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7530 (t) REVERT: B 485 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: B 570 ASP cc_start: 0.7662 (t0) cc_final: 0.7437 (t0) REVERT: B 685 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: B 845 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7566 (p90) REVERT: D 39 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: D 98 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7370 (tmm160) REVERT: D 151 TYR cc_start: 0.7309 (p90) cc_final: 0.6421 (p90) outliers start: 67 outliers final: 43 residues processed: 179 average time/residue: 0.0819 time to fit residues: 22.7643 Evaluate side-chains 164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 485 GLN Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** D 39 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 = 0.3997 r_free = 0.3997 target = 0.122825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091762 restraints weight = 31389.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094752 restraints weight = 14541.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096592 restraints weight = 9441.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097691 restraints weight = 7364.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098149 restraints weight = 6388.697| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12752 Z= 0.141 Angle : 0.624 11.027 17316 Z= 0.314 Chirality : 0.043 0.245 1919 Planarity : 0.004 0.043 2207 Dihedral : 4.908 58.448 1861 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.72 % Allowed : 26.92 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1557 helix: 1.09 (0.29), residues: 344 sheet: -0.39 (0.31), residues: 287 loop : -1.04 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.029 0.001 TYR C 49 PHE 0.012 0.001 PHE C 62 TRP 0.054 0.002 TRP D 47 HIS 0.006 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (12712) covalent geometry : angle 0.60523 / 0.31 (17235) SS BOND : bond 0.00256 / 0.19 ( 28) SS BOND : angle 2.28970 / 1.70 ( 56) hydrogen bonds : bond 0.03616 / 2.37 ( 374) hydrogen bonds : angle 5.06622 / 3.47 ( 999) metal coordination : bond 0.01703 / 0.87 ( 4) metal coordination : angle 2.72586 / 1.95 ( 1) link_BETA1-4 : bond 0.00427 / 0.28 ( 1) link_BETA1-4 : angle 0.79600 / 0.58 ( 3) link_NAG-ASN : bond 0.00392 / 0.25 ( 7) link_NAG-ASN : angle 2.50356 / 2.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: A 671 ASN cc_start: 0.8183 (m110) cc_final: 0.7299 (t0) REVERT: B 685 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: B 845 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7510 (p90) REVERT: C 143 GLU cc_start: 0.7719 (mp0) cc_final: 0.7514 (tp30) REVERT: D 39 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: D 47 TRP cc_start: 0.7632 (t60) cc_final: 0.7226 (t60) REVERT: D 73 ASP cc_start: 0.7740 (t0) cc_final: 0.7515 (t0) REVERT: D 98 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7315 (tmm160) REVERT: D 151 TYR cc_start: 0.7228 (p90) cc_final: 0.6343 (p90) outliers start: 65 outliers final: 51 residues processed: 183 average time/residue: 0.0825 time to fit residues: 23.6273 Evaluate side-chains 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 0.0370 chunk 59 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.123718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092404 restraints weight = 31662.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095469 restraints weight = 14634.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097313 restraints weight = 9495.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098413 restraints weight = 7411.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099084 restraints weight = 6437.982| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12752 Z= 0.117 Angle : 0.605 10.490 17316 Z= 0.302 Chirality : 0.043 0.222 1919 Planarity : 0.004 0.043 2207 Dihedral : 4.644 58.816 1861 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.92 % Allowed : 27.79 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1557 helix: 1.07 (0.29), residues: 350 sheet: -0.41 (0.30), residues: 290 loop : -1.00 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.029 0.001 TYR C 49 PHE 0.010 0.001 PHE C 62 TRP 0.032 0.001 TRP D 47 HIS 0.005 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12712) covalent geometry : angle 0.59499 / 0.30 (17235) SS BOND : bond 0.00205 / 0.15 ( 28) SS BOND : angle 1.45159 / 1.06 ( 56) hydrogen bonds : bond 0.03433 / 2.25 ( 374) hydrogen bonds : angle 5.02076 / 3.44 ( 999) metal coordination : bond 0.01509 / 0.83 ( 4) metal coordination : angle 1.25553 / 0.90 ( 1) link_BETA1-4 : bond 0.00464 / 0.31 ( 1) link_BETA1-4 : angle 0.80848 / 0.63 ( 3) link_NAG-ASN : bond 0.00449 / 0.24 ( 7) link_NAG-ASN : angle 2.32025 / 1.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7169 (m-40) REVERT: A 515 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7267 (t) REVERT: A 671 ASN cc_start: 0.8118 (m110) cc_final: 0.7367 (t0) REVERT: B 397 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 570 ASP cc_start: 0.7823 (t0) cc_final: 0.7481 (t0) REVERT: B 685 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: B 845 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7478 (p90) REVERT: D 47 TRP cc_start: 0.7685 (t60) cc_final: 0.7343 (t60) REVERT: D 98 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7289 (tmm160) REVERT: D 151 TYR cc_start: 0.7132 (p90) cc_final: 0.6353 (p90) outliers start: 54 outliers final: 42 residues processed: 170 average time/residue: 0.0788 time to fit residues: 21.0068 Evaluate side-chains 166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091329 restraints weight = 31728.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094346 restraints weight = 14739.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096161 restraints weight = 9593.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097270 restraints weight = 7524.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097873 restraints weight = 6531.110| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12752 Z= 0.144 Angle : 0.607 9.058 17316 Z= 0.303 Chirality : 0.043 0.208 1919 Planarity : 0.004 0.043 2207 Dihedral : 4.538 57.985 1861 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.99 % Allowed : 27.43 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1557 helix: 1.11 (0.29), residues: 350 sheet: -0.38 (0.31), residues: 288 loop : -1.02 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 38 TYR 0.028 0.001 TYR C 49 PHE 0.012 0.001 PHE B 841 TRP 0.033 0.001 TRP D 47 HIS 0.006 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (12712) covalent geometry : angle 0.60014 / 0.30 (17235) SS BOND : bond 0.00248 / 0.18 ( 28) SS BOND : angle 1.01612 / 0.74 ( 56) hydrogen bonds : bond 0.03542 / 2.32 ( 374) hydrogen bonds : angle 5.00272 / 3.43 ( 999) metal coordination : bond 0.01741 / 0.88 ( 4) metal coordination : angle 2.74275 / 1.96 ( 1) link_BETA1-4 : bond 0.00375 / 0.25 ( 1) link_BETA1-4 : angle 0.81440 / 0.61 ( 3) link_NAG-ASN : bond 0.00379 / 0.23 ( 7) link_NAG-ASN : angle 2.33787 / 1.95 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7170 (m-40) REVERT: A 671 ASN cc_start: 0.8177 (m110) cc_final: 0.7306 (t0) REVERT: B 397 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7736 (t80) REVERT: B 570 ASP cc_start: 0.7856 (t0) cc_final: 0.7507 (t0) REVERT: B 685 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: B 845 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7440 (p90) REVERT: D 47 TRP cc_start: 0.7802 (t60) cc_final: 0.7521 (t60) REVERT: D 151 TYR cc_start: 0.7152 (p90) cc_final: 0.6365 (p90) outliers start: 55 outliers final: 46 residues processed: 167 average time/residue: 0.0775 time to fit residues: 20.4001 Evaluate side-chains 166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 PHE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN D 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092401 restraints weight = 31408.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095416 restraints weight = 14600.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.097238 restraints weight = 9493.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098368 restraints weight = 7435.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098963 restraints weight = 6440.598| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12752 Z= 0.133 Angle : 0.606 9.116 17316 Z= 0.302 Chirality : 0.043 0.206 1919 Planarity : 0.004 0.043 2207 Dihedral : 4.461 57.645 1861 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.85 % Allowed : 27.65 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1557 helix: 1.05 (0.29), residues: 357 sheet: -0.40 (0.30), residues: 290 loop : -0.98 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.030 0.001 TYR D 80 PHE 0.010 0.001 PHE B 812 TRP 0.030 0.001 TRP D 47 HIS 0.006 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (12712) covalent geometry : angle 0.59958 / 0.30 (17235) SS BOND : bond 0.00227 / 0.17 ( 28) SS BOND : angle 0.96686 / 0.70 ( 56) hydrogen bonds : bond 0.03498 / 2.29 ( 374) hydrogen bonds : angle 4.97236 / 3.41 ( 999) metal coordination : bond 0.01720 / 0.89 ( 4) metal coordination : angle 2.44544 / 1.75 ( 1) link_BETA1-4 : bond 0.00418 / 0.28 ( 1) link_BETA1-4 : angle 0.84428 / 0.65 ( 3) link_NAG-ASN : bond 0.00377 / 0.23 ( 7) link_NAG-ASN : angle 2.26321 / 1.89 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.71 seconds wall clock time: 36 minutes 18.62 seconds (2178.62 seconds total)