Starting phenix.real_space_refine on Thu Sep 18 00:18:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_70127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_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 { model { file = "/net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_70127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_70127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_70127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o58_70127/09_2025/9o58_70127.map" } 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-2.0-5805/lib/python3.9/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, 86 Unusual residues: {' CA': 1, ' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 2.72, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 562.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 2.06 Time building geometry restraints manager: 1.32 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: 7.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.950 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 aren 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 covalent geometry : bond 0.00409 (12712) covalent geometry : angle 0.69781 (17235) SS BOND : bond 0.00194 ( 28) SS BOND : angle 1.20176 ( 56) hydrogen bonds : bond 0.27847 ( 374) hydrogen bonds : angle 8.81458 ( 999) metal coordination : bond 0.01192 ( 4) metal coordination : angle 2.15584 ( 1) link_BETA1-4 : bond 0.00713 ( 1) link_BETA1-4 : angle 1.00292 ( 3) link_NAG-ASN : bond 0.00748 ( 7) link_NAG-ASN : angle 9.71036 ( 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 : 0.402 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: 0.0863 time to fit residues: 17.8915 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 : 0.360 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.114511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085588 restraints weight = 30373.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088723 restraints weight = 15872.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088836 restraints weight = 10495.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089025 restraints weight = 9451.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089163 restraints weight = 8954.319| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12752 Z= 0.175 Angle : 0.639 9.781 17316 Z= 0.327 Chirality : 0.044 0.228 1919 Planarity : 0.004 0.046 2207 Dihedral : 5.706 54.874 1865 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.64 % Allowed : 24.89 % Favored : 70.46 % 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 aren not related in a simple way. whole: -0.95 (0.21), residues: 1557 helix: 0.08 (0.27), residues: 362 sheet: -0.13 (0.31), residues: 277 loop : -1.08 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.025 0.002 TYR C 49 PHE 0.018 0.002 PHE A 664 TRP 0.032 0.001 TRP D 47 HIS 0.004 0.001 HIS B 773 Details of bonding type rmsd covalent geometry : bond 0.00401 (12712) covalent geometry : angle 0.61942 (17235) SS BOND : bond 0.00270 ( 28) SS BOND : angle 1.05368 ( 56) hydrogen bonds : bond 0.05453 ( 374) hydrogen bonds : angle 6.25602 ( 999) metal coordination : bond 0.01964 ( 4) metal coordination : angle 4.74646 ( 1) link_BETA1-4 : bond 0.00479 ( 1) link_BETA1-4 : angle 0.73594 ( 3) link_NAG-ASN : bond 0.00489 ( 7) link_NAG-ASN : angle 4.14594 ( 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 184 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 120 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7960 (mmm) cc_final: 0.7497 (mmp) REVERT: A 535 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: B 485 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: D 57 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7193 (mmt) REVERT: D 73 ASP cc_start: 0.7862 (t0) cc_final: 0.7653 (t0) outliers start: 64 outliers final: 30 residues processed: 172 average time/residue: 0.0754 time to fit residues: 20.7181 Evaluate side-chains 142 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 75 LEU 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 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 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: 7.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 535 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085076 restraints weight = 30791.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088387 restraints weight = 15388.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088309 restraints weight = 10136.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088610 restraints weight = 9033.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088656 restraints weight = 8467.815| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12752 Z= 0.169 Angle : 0.606 9.904 17316 Z= 0.306 Chirality : 0.043 0.237 1919 Planarity : 0.004 0.045 2207 Dihedral : 5.531 54.967 1861 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.15 % Allowed : 24.67 % Favored : 70.17 % 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 aren not related in a simple way. whole: -0.83 (0.21), residues: 1557 helix: 0.44 (0.28), residues: 355 sheet: -0.22 (0.31), residues: 277 loop : -1.06 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 401 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 0.004 0.001 HIS B 565 Details of bonding type rmsd covalent geometry : bond 0.00391 (12712) covalent geometry : angle 0.58721 (17235) SS BOND : bond 0.00272 ( 28) SS BOND : angle 1.07606 ( 56) hydrogen bonds : bond 0.04755 ( 374) hydrogen bonds : angle 5.82236 ( 999) metal coordination : bond 0.01895 ( 4) metal coordination : angle 4.21923 ( 1) link_BETA1-4 : bond 0.00835 ( 1) link_BETA1-4 : angle 0.97480 ( 3) link_NAG-ASN : bond 0.00417 ( 7) link_NAG-ASN : angle 3.96836 ( 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 188 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 117 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8580 (mmt) cc_final: 0.8358 (mmt) REVERT: A 498 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: B 485 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: B 685 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: C 189 HIS cc_start: 0.5509 (OUTLIER) cc_final: 0.5218 (t70) REVERT: D 39 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7416 (tp-100) REVERT: D 73 ASP cc_start: 0.7885 (t0) cc_final: 0.7650 (t0) outliers start: 71 outliers final: 37 residues processed: 177 average time/residue: 0.0898 time to fit residues: 25.3224 Evaluate side-chains 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 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 498 ASN 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 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 733 VAL Chi-restraints excluded: chain B residue 837 THR 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 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 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: 0.9980 chunk 131 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 524 ASN A 560 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.113915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083858 restraints weight = 30599.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086504 restraints weight = 15618.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088166 restraints weight = 10530.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089130 restraints weight = 8362.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089758 restraints weight = 7348.025| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12752 Z= 0.163 Angle : 0.595 9.228 17316 Z= 0.301 Chirality : 0.043 0.234 1919 Planarity : 0.004 0.044 2207 Dihedral : 5.432 56.141 1861 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.95 % Allowed : 24.53 % Favored : 69.52 % 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 aren not related in a simple way. whole: -0.76 (0.21), residues: 1557 helix: 0.69 (0.28), residues: 349 sheet: -0.26 (0.31), residues: 277 loop : -1.06 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.026 0.001 TYR C 49 PHE 0.013 0.001 PHE B 812 TRP 0.017 0.001 TRP B 832 HIS 0.003 0.001 HIS B 565 Details of bonding type rmsd covalent geometry : bond 0.00380 (12712) covalent geometry : angle 0.57990 (17235) SS BOND : bond 0.00343 ( 28) SS BOND : angle 1.08007 ( 56) hydrogen bonds : bond 0.04262 ( 374) hydrogen bonds : angle 5.57277 ( 999) metal coordination : bond 0.01843 ( 4) metal coordination : angle 4.66085 ( 1) link_BETA1-4 : bond 0.00323 ( 1) link_BETA1-4 : angle 0.77846 ( 3) link_NAG-ASN : bond 0.00411 ( 7) link_NAG-ASN : angle 3.42439 ( 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 199 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 117 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6169 (t) REVERT: B 485 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: B 685 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: B 845 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7462 (p90) REVERT: C 61 ARG cc_start: 0.8908 (ptp-170) cc_final: 0.8706 (ptp-170) REVERT: C 189 HIS cc_start: 0.5449 (OUTLIER) cc_final: 0.5157 (t70) REVERT: D 39 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7392 (tp-100) REVERT: D 47 TRP cc_start: 0.8252 (t60) cc_final: 0.7929 (t60) REVERT: D 57 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7261 (mmt) REVERT: D 73 ASP cc_start: 0.7861 (t0) cc_final: 0.7629 (t0) outliers start: 82 outliers final: 48 residues processed: 186 average time/residue: 0.0795 time to fit residues: 23.3508 Evaluate side-chains 169 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 VAL 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 452 ASN Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 582 CYS 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 682 ILE 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 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 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 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 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 83 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 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 79 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083298 restraints weight = 30754.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086547 restraints weight = 15219.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086590 restraints weight = 10101.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086671 restraints weight = 9193.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086756 restraints weight = 8804.496| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12752 Z= 0.226 Angle : 0.639 9.615 17316 Z= 0.322 Chirality : 0.045 0.228 1919 Planarity : 0.004 0.044 2207 Dihedral : 5.500 59.935 1861 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.60 % Allowed : 24.46 % Favored : 68.94 % 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 aren not related in a simple way. whole: -0.79 (0.21), residues: 1557 helix: 0.73 (0.29), residues: 349 sheet: -0.41 (0.30), residues: 279 loop : -1.06 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 401 TYR 0.027 0.002 TYR C 49 PHE 0.019 0.002 PHE B 841 TRP 0.020 0.001 TRP B 832 HIS 0.005 0.001 HIS B 565 Details of bonding type rmsd covalent geometry : bond 0.00525 (12712) covalent geometry : angle 0.62202 (17235) SS BOND : bond 0.00349 ( 28) SS BOND : angle 1.29148 ( 56) hydrogen bonds : bond 0.04247 ( 374) hydrogen bonds : angle 5.45266 ( 999) metal coordination : bond 0.02440 ( 4) metal coordination : angle 5.42337 ( 1) link_BETA1-4 : bond 0.00319 ( 1) link_BETA1-4 : angle 0.90401 ( 3) link_NAG-ASN : bond 0.00422 ( 7) link_NAG-ASN : angle 3.63684 ( 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 215 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 124 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 411 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8385 (t80) REVERT: A 498 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7063 (m-40) REVERT: B 397 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 485 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: B 685 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: B 845 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7485 (p90) REVERT: C 61 ARG cc_start: 0.9007 (ptp-170) cc_final: 0.8644 (ptp-170) REVERT: C 189 HIS cc_start: 0.5402 (OUTLIER) cc_final: 0.5128 (t70) REVERT: D 39 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7314 (tp-100) REVERT: D 47 TRP cc_start: 0.8333 (t60) cc_final: 0.7930 (t60) REVERT: D 57 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: D 73 ASP cc_start: 0.7973 (t0) cc_final: 0.7694 (t0) outliers start: 91 outliers final: 56 residues processed: 199 average time/residue: 0.0870 time to fit residues: 26.6700 Evaluate side-chains 178 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 469 CYS 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 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 782 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 2 VAL 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 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: 2.9990 chunk 92 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086125 restraints weight = 30546.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088343 restraints weight = 15351.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089248 restraints weight = 10478.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089345 restraints weight = 9046.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089529 restraints weight = 8873.719| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12752 Z= 0.125 Angle : 0.605 11.406 17316 Z= 0.303 Chirality : 0.043 0.251 1919 Planarity : 0.004 0.045 2207 Dihedral : 5.270 59.650 1861 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.86 % Allowed : 26.27 % Favored : 68.87 % 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 aren not related in a simple way. whole: -0.66 (0.21), residues: 1557 helix: 1.04 (0.29), residues: 342 sheet: -0.39 (0.31), residues: 283 loop : -1.04 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.028 0.001 TYR C 49 PHE 0.011 0.001 PHE B 812 TRP 0.028 0.001 TRP D 160 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00293 (12712) covalent geometry : angle 0.58942 (17235) SS BOND : bond 0.00220 ( 28) SS BOND : angle 1.61922 ( 56) hydrogen bonds : bond 0.03797 ( 374) hydrogen bonds : angle 5.25781 ( 999) metal coordination : bond 0.01595 ( 4) metal coordination : angle 1.73222 ( 1) link_BETA1-4 : bond 0.00319 ( 1) link_BETA1-4 : angle 0.79592 ( 3) link_NAG-ASN : bond 0.00389 ( 7) link_NAG-ASN : angle 3.09555 ( 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 191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 124 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8117 (ttp-170) REVERT: A 411 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8350 (t80) REVERT: A 582 CYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6127 (t) REVERT: B 485 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: B 570 ASP cc_start: 0.7679 (t0) cc_final: 0.7389 (t0) REVERT: B 594 GLU cc_start: 0.7915 (pp20) cc_final: 0.7667 (pp20) REVERT: B 685 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: B 845 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7473 (p90) REVERT: C 189 HIS cc_start: 0.5022 (OUTLIER) cc_final: 0.4816 (t70) REVERT: D 39 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: D 73 ASP cc_start: 0.7721 (t0) cc_final: 0.7515 (t0) REVERT: D 98 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7413 (tmm160) outliers start: 67 outliers final: 43 residues processed: 180 average time/residue: 0.0922 time to fit residues: 25.3160 Evaluate side-chains 167 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 241 ARG 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 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 591 CYS 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 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 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 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 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 83 MET Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 VAL 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: 5.9990 chunk 44 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084931 restraints weight = 30424.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088032 restraints weight = 15860.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088357 restraints weight = 10458.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088418 restraints weight = 9466.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088498 restraints weight = 9081.101| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12752 Z= 0.149 Angle : 0.610 10.806 17316 Z= 0.305 Chirality : 0.044 0.275 1919 Planarity : 0.004 0.044 2207 Dihedral : 5.083 59.412 1861 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.86 % Allowed : 26.85 % Favored : 68.29 % 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 aren not related in a simple way. whole: -0.68 (0.21), residues: 1557 helix: 1.04 (0.29), residues: 343 sheet: -0.39 (0.31), residues: 283 loop : -1.06 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.028 0.001 TYR C 49 PHE 0.012 0.001 PHE B 812 TRP 0.048 0.002 TRP D 47 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00353 (12712) covalent geometry : angle 0.59137 (17235) SS BOND : bond 0.00313 ( 28) SS BOND : angle 1.67617 ( 56) hydrogen bonds : bond 0.03724 ( 374) hydrogen bonds : angle 5.14655 ( 999) metal coordination : bond 0.01667 ( 4) metal coordination : angle 3.14118 ( 1) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 0.78854 ( 3) link_NAG-ASN : bond 0.00361 ( 7) link_NAG-ASN : angle 3.40785 ( 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 192 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8106 (ttp-170) REVERT: A 411 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8320 (t80) REVERT: A 498 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6933 (m-40) REVERT: A 671 ASN cc_start: 0.8242 (m110) cc_final: 0.7362 (t0) REVERT: B 397 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7750 (t80) REVERT: B 485 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7849 (mp-120) REVERT: B 570 ASP cc_start: 0.7670 (t0) cc_final: 0.7425 (t0) REVERT: B 594 GLU cc_start: 0.7981 (pp20) cc_final: 0.7711 (pp20) REVERT: B 685 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: B 845 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7464 (p90) REVERT: C 189 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.4898 (t70) REVERT: D 39 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: D 47 TRP cc_start: 0.7689 (t60) cc_final: 0.7362 (t60) REVERT: D 73 ASP cc_start: 0.7692 (t0) cc_final: 0.7484 (t0) REVERT: D 151 TYR cc_start: 0.7330 (p90) cc_final: 0.6435 (p90) outliers start: 67 outliers final: 46 residues processed: 180 average time/residue: 0.0777 time to fit residues: 21.8693 Evaluate side-chains 170 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 593 CYS 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 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 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 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 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 83 MET Chi-restraints excluded: chain D residue 117 VAL 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: 0.8980 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 chunk 50 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3835 r_free = 0.3835 target = 0.115667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086209 restraints weight = 30336.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088859 restraints weight = 15524.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090529 restraints weight = 10475.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091540 restraints weight = 8309.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092077 restraints weight = 7258.735| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2150 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= 0.112 Angle : 0.593 9.013 17316 Z= 0.296 Chirality : 0.043 0.281 1919 Planarity : 0.004 0.044 2207 Dihedral : 4.782 59.984 1861 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.64 % Allowed : 26.85 % 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 aren not related in a simple way. whole: -0.60 (0.22), residues: 1557 helix: 1.06 (0.29), residues: 344 sheet: -0.39 (0.31), residues: 291 loop : -0.98 (0.21), residues: 922 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 B 749 TRP 0.028 0.001 TRP D 47 HIS 0.006 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00263 (12712) covalent geometry : angle 0.58058 (17235) SS BOND : bond 0.00186 ( 28) SS BOND : angle 1.30775 ( 56) hydrogen bonds : bond 0.03465 ( 374) hydrogen bonds : angle 5.06441 ( 999) metal coordination : bond 0.01385 ( 4) metal coordination : angle 0.82626 ( 1) link_BETA1-4 : bond 0.00354 ( 1) link_BETA1-4 : angle 0.74362 ( 3) link_NAG-ASN : bond 0.00415 ( 7) link_NAG-ASN : angle 2.95481 ( 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: 64 poor density : 125 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.8112 (m110) cc_final: 0.7415 (t0) REVERT: B 397 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7647 (t80) REVERT: B 570 ASP cc_start: 0.7573 (t0) cc_final: 0.7317 (t0) REVERT: B 594 GLU cc_start: 0.7976 (pp20) cc_final: 0.7729 (pp20) REVERT: B 685 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: B 845 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7463 (p90) REVERT: C 189 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.4882 (t70) REVERT: D 47 TRP cc_start: 0.7693 (t60) cc_final: 0.7419 (t60) REVERT: D 98 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7419 (tmm160) REVERT: D 151 TYR cc_start: 0.7355 (p90) cc_final: 0.6446 (p90) outliers start: 64 outliers final: 44 residues processed: 180 average time/residue: 0.0890 time to fit residues: 24.5422 Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 333 CYS 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 483 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 615 VAL 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 508 CYS 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 782 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 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 98 ARG Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 133 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: 0.2980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 111 optimal weight: 0.0010 chunk 81 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4015 r_free = 0.4015 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092658 restraints weight = 31701.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095693 restraints weight = 14562.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097553 restraints weight = 9395.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098670 restraints weight = 7318.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099234 restraints weight = 6331.328| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12752 Z= 0.117 Angle : 0.626 10.958 17316 Z= 0.311 Chirality : 0.043 0.361 1919 Planarity : 0.004 0.044 2207 Dihedral : 4.660 59.743 1861 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.14 % Allowed : 27.43 % Favored : 68.43 % 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 aren not related in a simple way. whole: -0.58 (0.22), residues: 1557 helix: 1.16 (0.29), residues: 344 sheet: -0.37 (0.31), residues: 291 loop : -1.01 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 489 TYR 0.029 0.001 TYR C 49 PHE 0.009 0.001 PHE B 749 TRP 0.021 0.001 TRP D 47 HIS 0.005 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00277 (12712) covalent geometry : angle 0.60728 (17235) SS BOND : bond 0.00157 ( 28) SS BOND : angle 1.90869 ( 56) hydrogen bonds : bond 0.03436 ( 374) hydrogen bonds : angle 4.98066 ( 999) metal coordination : bond 0.01373 ( 4) metal coordination : angle 1.16184 ( 1) link_BETA1-4 : bond 0.00429 ( 1) link_BETA1-4 : angle 0.73789 ( 3) link_NAG-ASN : bond 0.00461 ( 7) link_NAG-ASN : angle 3.21099 ( 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 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.8126 (m110) cc_final: 0.7368 (t0) REVERT: B 570 ASP cc_start: 0.7733 (t0) cc_final: 0.7509 (t0) REVERT: B 594 GLU cc_start: 0.7908 (pp20) cc_final: 0.7608 (pp20) REVERT: B 685 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: B 845 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7441 (p90) REVERT: C 189 HIS cc_start: 0.5328 (OUTLIER) cc_final: 0.5119 (t70) REVERT: D 47 TRP cc_start: 0.7797 (t60) cc_final: 0.7523 (t60) REVERT: D 98 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7293 (tmm160) REVERT: D 151 TYR cc_start: 0.7199 (p90) cc_final: 0.6390 (p90) outliers start: 57 outliers final: 43 residues processed: 172 average time/residue: 0.0825 time to fit residues: 22.3950 Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 333 CYS 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 483 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 615 VAL 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 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 699 LEU 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 23 CYS Chi-restraints excluded: chain C residue 69 THR 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 11 LEU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 19 ARG 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 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 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 21 optimal weight: 0.0570 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 152 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.093645 restraints weight = 31536.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096663 restraints weight = 14408.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098520 restraints weight = 9245.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099638 restraints weight = 7173.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.100187 restraints weight = 6197.457| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2357 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= 0.109 Angle : 0.602 8.793 17316 Z= 0.299 Chirality : 0.043 0.366 1919 Planarity : 0.004 0.044 2207 Dihedral : 4.409 58.893 1861 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.19 % Allowed : 28.30 % 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 aren not related in a simple way. whole: -0.53 (0.22), residues: 1557 helix: 1.10 (0.29), residues: 357 sheet: -0.21 (0.31), residues: 288 loop : -1.00 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.028 0.001 TYR C 49 PHE 0.013 0.001 PHE A 687 TRP 0.021 0.001 TRP B 832 HIS 0.004 0.000 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00252 (12712) covalent geometry : angle 0.59469 (17235) SS BOND : bond 0.00225 ( 28) SS BOND : angle 1.07364 ( 56) hydrogen bonds : bond 0.03245 ( 374) hydrogen bonds : angle 4.86511 ( 999) metal coordination : bond 0.01419 ( 4) metal coordination : angle 0.89149 ( 1) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 0.76604 ( 3) link_NAG-ASN : bond 0.00735 ( 7) link_NAG-ASN : angle 2.34567 ( 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 170 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.8089 (m110) cc_final: 0.7342 (t0) REVERT: B 594 GLU cc_start: 0.7896 (pp20) cc_final: 0.7565 (pp20) REVERT: B 685 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: B 845 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7374 (p90) REVERT: D 47 TRP cc_start: 0.7848 (t60) cc_final: 0.7624 (t60) REVERT: D 77 ASN cc_start: 0.8390 (m-40) cc_final: 0.7814 (p0) REVERT: D 151 TYR cc_start: 0.7182 (p90) cc_final: 0.6313 (p90) outliers start: 44 outliers final: 41 residues processed: 165 average time/residue: 0.0824 time to fit residues: 21.3899 Evaluate side-chains 160 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 333 CYS 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 483 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 615 VAL 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 519 THR 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 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 845 PHE Chi-restraints excluded: chain C residue 69 THR 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 52 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 149 optimal weight: 40.0000 chunk 97 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091475 restraints weight = 31408.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094449 restraints weight = 14605.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096295 restraints weight = 9479.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097420 restraints weight = 7392.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097884 restraints weight = 6393.172| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12752 Z= 0.151 Angle : 0.626 11.446 17316 Z= 0.311 Chirality : 0.044 0.366 1919 Planarity : 0.004 0.043 2207 Dihedral : 4.410 59.125 1861 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.56 % Allowed : 28.37 % Favored : 68.07 % 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 aren not related in a simple way. whole: -0.54 (0.22), residues: 1557 helix: 1.09 (0.29), residues: 357 sheet: -0.23 (0.31), residues: 286 loop : -1.01 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 489 TYR 0.031 0.001 TYR C 173 PHE 0.013 0.001 PHE B 841 TRP 0.024 0.001 TRP D 47 HIS 0.006 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00358 (12712) covalent geometry : angle 0.61780 (17235) SS BOND : bond 0.00263 ( 28) SS BOND : angle 1.24644 ( 56) hydrogen bonds : bond 0.03436 ( 374) hydrogen bonds : angle 4.86603 ( 999) metal coordination : bond 0.01782 ( 4) metal coordination : angle 3.65518 ( 1) link_BETA1-4 : bond 0.00230 ( 1) link_BETA1-4 : angle 0.86025 ( 3) link_NAG-ASN : bond 0.00541 ( 7) link_NAG-ASN : angle 2.25024 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.01 seconds wall clock time: 39 minutes 44.40 seconds (2384.40 seconds total)