Starting phenix.real_space_refine on Sat Feb 7 02:31:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef4_47969/02_2026/9ef4_47969_trim.cif" } resolution = 3.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 118 5.16 5 C 9115 2.51 5 N 2439 2.21 5 O 2803 1.98 5 H 13904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28379 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 409 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "D" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 295 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 409 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "F" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 315 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 13355 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 43, 'TRANS': 807} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 13358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 13358 Classifications: {'peptide': 851} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 806} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.15, per 1000 atoms: 0.18 Number of scatterers: 28379 At special positions: 0 Unit cell: (155.1, 100.1, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 O 2803 8.00 N 2439 7.00 C 9115 6.00 H 13904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS D 24 " distance=2.02 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 15 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS F 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 10 " - pdb=" SG CYS F 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 539 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 770 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 873 " - pdb=" SG CYS B 873 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A1258 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 357 " distance=2.04 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 539 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 643 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 770 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1188 " 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 NAG-ASN " NAG A2201 " - " ASN A 356 " " NAG A2202 " - " ASN A 376 " " NAG A2203 " - " ASN A 751 " " NAG A2204 " - " ASN A 810 " " NAG A2205 " - " ASN A 824 " " NAG A2206 " - " ASN A 864 " " NAG A2207 " - " ASN A 898 " " NAG A2208 " - " ASN A 946 " " NAG A2209 " - " ASN A1147 " " NAG B2201 " - " ASN B 356 " " NAG B2202 " - " ASN B 376 " " NAG B2203 " - " ASN B 810 " " NAG B2204 " - " ASN B 824 " " NAG B2205 " - " ASN B 864 " " NAG B2206 " - " ASN B 898 " " NAG B2207 " - " ASN B 946 " " NAG B2208 " - " ASN B1147 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 715.5 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 38 sheets defined 15.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 22 through 25 removed outlier: 3.630A pdb=" N LEU D 25 " --> pdb=" O ILE D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 25' Processing helix chain 'E' and resid 20 through 32 removed outlier: 3.589A pdb=" N VAL E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 10 Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.560A pdb=" N ILE A 459 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.680A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.616A pdb=" N GLU A 469 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 470 " --> pdb=" O GLU A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 466 through 470' Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.603A pdb=" N ARG A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 486 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 487 " --> pdb=" O CYS A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 487' Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.530A pdb=" N THR A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.908A pdb=" N GLU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.704A pdb=" N LYS A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.551A pdb=" N ILE A 774 " --> pdb=" O CYS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 781 removed outlier: 3.767A pdb=" N LEU A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1044 removed outlier: 3.832A pdb=" N VAL A1029 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1044 " --> pdb=" O GLN A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1178 Processing helix chain 'A' and resid 1264 through 1268 Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.966A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.564A pdb=" N ARG B 536 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 639 through 642 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 684 through 694 Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 846 through 848 No H-bonds generated for 'chain 'B' and resid 846 through 848' Processing helix chain 'B' and resid 1026 through 1044 removed outlier: 3.794A pdb=" N PHE B1044 " --> pdb=" O GLN B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1178 Processing helix chain 'B' and resid 1263 through 1268 Processing sheet with id=AA1, first strand: chain 'A' and resid 342 through 346 removed outlier: 6.466A pdb=" N MET A 342 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP A 367 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 344 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 369 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 346 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 394 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 389 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR A 424 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 391 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.507A pdb=" N VAL A 385 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 554 removed outlier: 5.163A pdb=" N LEU A 551 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N CYS A 567 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 553 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA5, first strand: chain 'A' and resid 584 through 587 Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 603 Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 614 Processing sheet with id=AA8, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.934A pdb=" N ILE A 667 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 673 through 674 removed outlier: 5.700A pdb=" N LEU A 673 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 703 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU A 739 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY A 760 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 736 " --> pdb=" O GLY A 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 764 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 807 through 809 removed outlier: 5.692A pdb=" N ALA A 807 " --> pdb=" O GLU A 916 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 816 removed outlier: 6.662A pdb=" N MET A 822 " --> pdb=" O GLN A 814 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 830 through 831 removed outlier: 6.360A pdb=" N GLU A 830 " --> pdb=" O PHE A 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AB6, first strand: chain 'A' and resid 933 through 939 removed outlier: 4.809A pdb=" N GLU A 934 " --> pdb=" O SER A 950 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 950 " --> pdb=" O GLU A 934 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 3.751A pdb=" N VAL A1139 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLU A1138 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 961 " --> pdb=" O CYS A1169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1208 through 1214 removed outlier: 5.770A pdb=" N ASP A1209 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A1229 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1255 through 1259 Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1259 removed outlier: 3.630A pdb=" N GLY A1277 " --> pdb=" O VAL A1302 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 332 removed outlier: 7.315A pdb=" N ARG B 331 " --> pdb=" O CYS B 564 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 342 through 345 removed outlier: 6.837A pdb=" N VAL B 394 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 389 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR B 424 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 391 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ARG B 446 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 422 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU B 448 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR B 424 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC5, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AC6, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AC7, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.555A pdb=" N ARG B 590 " --> pdb=" O PHE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 601 through 603 Processing sheet with id=AC9, first strand: chain 'B' and resid 612 through 614 Processing sheet with id=AD1, first strand: chain 'B' and resid 626 through 628 Processing sheet with id=AD2, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.600A pdb=" N ILE B 667 " --> pdb=" O LYS B 698 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 673 through 675 removed outlier: 3.821A pdb=" N MET B 704 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 703 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR B 734 " --> pdb=" O GLY B 760 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE B 762 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 736 " --> pdb=" O PHE B 762 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 807 through 809 removed outlier: 5.546A pdb=" N ALA B 807 " --> pdb=" O GLU B 916 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 811 through 816 removed outlier: 6.637A pdb=" N MET B 822 " --> pdb=" O GLN B 814 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 830 through 831 removed outlier: 6.360A pdb=" N GLU B 830 " --> pdb=" O PHE B 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AD8, first strand: chain 'B' and resid 933 through 939 removed outlier: 4.835A pdb=" N GLU B 934 " --> pdb=" O SER B 950 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER B 950 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 3.733A pdb=" N VAL B1139 " --> pdb=" O ASP B1129 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU B1138 " --> pdb=" O LEU B 968 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 961 " --> pdb=" O CYS B1169 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1208 through 1214 removed outlier: 5.505A pdb=" N ASP B1209 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B1229 " --> pdb=" O ASP B1209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1255 through 1259 removed outlier: 4.160A pdb=" N GLY B1277 " --> pdb=" O VAL B1302 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B1298 " --> pdb=" O PHE B1281 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13902 1.03 - 1.23: 288 1.23 - 1.43: 5834 1.43 - 1.63: 8501 1.63 - 1.82: 154 Bond restraints: 28679 Sorted by residual: bond pdb=" N PRO B1304 " pdb=" CA PRO B1304 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.31e-02 5.83e+03 1.09e+01 bond pdb=" N GLY D 4 " pdb=" CA GLY D 4 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.59e+00 bond pdb=" N GLY F 4 " pdb=" CA GLY F 4 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.97e+00 bond pdb=" N PRO A1304 " pdb=" CA PRO A1304 " ideal model delta sigma weight residual 1.465 1.505 -0.040 2.03e-02 2.43e+03 3.89e+00 bond pdb=" N LEU C 12 " pdb=" CA LEU C 12 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 ... (remaining 28674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 49394 1.31 - 2.63: 2149 2.63 - 3.94: 189 3.94 - 5.26: 25 5.26 - 6.57: 3 Bond angle restraints: 51760 Sorted by residual: angle pdb=" N VAL A 986 " pdb=" CA VAL A 986 " pdb=" C VAL A 986 " ideal model delta sigma weight residual 111.62 107.32 4.30 7.90e-01 1.60e+00 2.97e+01 angle pdb=" C ARG B1200 " pdb=" N LYS B1201 " pdb=" CA LYS B1201 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" CA ALA B 988 " pdb=" C ALA B 988 " pdb=" O ALA B 988 " ideal model delta sigma weight residual 121.98 117.90 4.08 1.13e+00 7.83e-01 1.30e+01 angle pdb=" C ASN B 356 " pdb=" N CYS B 357 " pdb=" CA CYS B 357 " ideal model delta sigma weight residual 122.77 118.01 4.76 1.33e+00 5.65e-01 1.28e+01 angle pdb=" N ASP A1205 " pdb=" CA ASP A1205 " pdb=" CB ASP A1205 " ideal model delta sigma weight residual 114.17 110.31 3.86 1.14e+00 7.69e-01 1.15e+01 ... (remaining 51755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 12459 17.67 - 35.35: 1079 35.35 - 53.02: 270 53.02 - 70.70: 102 70.70 - 88.37: 37 Dihedral angle restraints: 13947 sinusoidal: 7789 harmonic: 6158 Sorted by residual: dihedral pdb=" CB CYS A 454 " pdb=" SG CYS A 454 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -169.44 83.44 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 554 " pdb=" CB CYS A 554 " ideal model delta sinusoidal sigma weight residual 93.00 159.35 -66.35 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS B 454 " pdb=" SG CYS B 454 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual 93.00 149.34 -56.34 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 13944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1921 0.059 - 0.117: 294 0.117 - 0.176: 50 0.176 - 0.235: 1 0.235 - 0.293: 4 Chirality restraints: 2270 Sorted by residual: chirality pdb=" C1 NAG A2209 " pdb=" ND2 ASN A1147 " pdb=" C2 NAG A2209 " pdb=" O5 NAG A2209 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG A2208 " pdb=" ND2 ASN A 946 " pdb=" C2 NAG A2208 " pdb=" O5 NAG A2208 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG A2205 " pdb=" ND2 ASN A 824 " pdb=" C2 NAG A2205 " pdb=" O5 NAG A2205 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2267 not shown) Planarity restraints: 4279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1303 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C GLU B1303 " 0.075 2.00e-02 2.50e+03 pdb=" O GLU B1303 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO B1304 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1303 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C GLU A1303 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU A1303 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A1304 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1303 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A1304 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1304 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1304 " -0.036 5.00e-02 4.00e+02 ... (remaining 4276 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 969 2.12 - 2.74: 50990 2.74 - 3.36: 80179 3.36 - 3.98: 101685 3.98 - 4.60: 156923 Nonbonded interactions: 390746 Sorted by model distance: nonbonded pdb=" OE1 GLU B 646 " pdb=" H GLU B 646 " model vdw 1.501 2.450 nonbonded pdb=" O ASN E 16 " pdb=" HG1 THR F 14 " model vdw 1.530 2.450 nonbonded pdb=" O THR B1160 " pdb="HH21 ARG B1200 " model vdw 1.540 2.450 nonbonded pdb=" OD1 ASP A 541 " pdb=" H THR A 544 " model vdw 1.549 2.450 nonbonded pdb=" O ASN B1235 " pdb=" HG SER B1287 " model vdw 1.552 2.450 ... (remaining 390741 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 328 through 2208) selection = (chain 'B' and (resid 328 through 750 or (resid 751 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3 or name HD21)) or resid 752 through 980 or (resid 981 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me HA or name HB2 or name HB3)) or resid 982 through 1257 or (resid 1258 and (na \ me N or name CA or name C or name O or name CB or name SG or name H or name HA o \ r name HB2 or name HB3)) or resid 1259 through 2208)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 10 through 24 or (resid 25 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 26)) } 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 0.043 14832 Z= 0.197 Angle : 0.679 7.960 20125 Z= 0.388 Chirality : 0.046 0.293 2270 Planarity : 0.004 0.067 2568 Dihedral : 14.041 87.551 5800 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.91 % Favored : 90.64 % Rotamer: Outliers : 0.49 % Allowed : 11.91 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1774 helix: -1.12 (0.37), residues: 156 sheet: -0.70 (0.26), residues: 336 loop : -1.46 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 757 TYR 0.016 0.001 TYR B 737 PHE 0.035 0.001 PHE B 404 TRP 0.007 0.001 TRP B 522 HIS 0.006 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00384 (14775) covalent geometry : angle 0.66790 (19994) SS BOND : bond 0.00262 ( 40) SS BOND : angle 0.75973 ( 80) hydrogen bonds : bond 0.23931 ( 336) hydrogen bonds : angle 9.56012 ( 876) link_NAG-ASN : bond 0.00258 ( 17) link_NAG-ASN : angle 2.44558 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 90 average time/residue: 0.2269 time to fit residues: 32.4286 Evaluate side-chains 90 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 942 ASP Chi-restraints excluded: chain B residue 1160 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1235 ASN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.113299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.079504 restraints weight = 130620.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.083760 restraints weight = 58359.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086626 restraints weight = 36549.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.088342 restraints weight = 27387.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.089180 restraints weight = 22989.015| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14832 Z= 0.146 Angle : 0.611 6.475 20125 Z= 0.325 Chirality : 0.046 0.263 2270 Planarity : 0.004 0.037 2568 Dihedral : 6.964 52.177 2313 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.68 % Favored : 90.87 % Rotamer: Outliers : 0.93 % Allowed : 11.85 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1774 helix: -0.71 (0.38), residues: 158 sheet: -1.01 (0.26), residues: 306 loop : -1.41 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1200 TYR 0.015 0.001 TYR A 902 PHE 0.016 0.001 PHE B1165 TRP 0.004 0.001 TRP B1228 HIS 0.007 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00321 (14775) covalent geometry : angle 0.60133 (19994) SS BOND : bond 0.00240 ( 40) SS BOND : angle 0.79372 ( 80) hydrogen bonds : bond 0.05014 ( 336) hydrogen bonds : angle 7.81799 ( 876) link_NAG-ASN : bond 0.00213 ( 17) link_NAG-ASN : angle 2.11645 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: A 883 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 342 MET cc_start: 0.7015 (tpp) cc_final: 0.6568 (tpp) REVERT: B 963 PHE cc_start: 0.6606 (t80) cc_final: 0.6311 (t80) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.2296 time to fit residues: 34.7853 Evaluate side-chains 96 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 1160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** B 892 ASN ** 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 = 0.4281 r_free = 0.4281 target = 0.111794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.078259 restraints weight = 130370.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.082445 restraints weight = 58227.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.085196 restraints weight = 36368.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086814 restraints weight = 27352.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087622 restraints weight = 23062.647| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14832 Z= 0.219 Angle : 0.617 6.139 20125 Z= 0.329 Chirality : 0.045 0.253 2270 Planarity : 0.004 0.039 2568 Dihedral : 6.959 53.007 2308 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.24 % Favored : 90.30 % Rotamer: Outliers : 1.30 % Allowed : 12.04 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1774 helix: -0.89 (0.39), residues: 158 sheet: -1.28 (0.25), residues: 348 loop : -1.65 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.018 0.002 TYR A 737 PHE 0.017 0.001 PHE B 762 TRP 0.007 0.001 TRP B 949 HIS 0.006 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00473 (14775) covalent geometry : angle 0.60793 (19994) SS BOND : bond 0.00401 ( 40) SS BOND : angle 0.86847 ( 80) hydrogen bonds : bond 0.04464 ( 336) hydrogen bonds : angle 7.48109 ( 876) link_NAG-ASN : bond 0.00363 ( 17) link_NAG-ASN : angle 2.01336 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 MET cc_start: 0.8795 (mmm) cc_final: 0.8582 (mmm) REVERT: A 1124 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.5038 (p90) REVERT: B 963 PHE cc_start: 0.6559 (t80) cc_final: 0.6213 (t80) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 0.2193 time to fit residues: 34.5244 Evaluate side-chains 97 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 1160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 ASN ** 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 = 0.4323 r_free = 0.4323 target = 0.113169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081678 restraints weight = 144758.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.085772 restraints weight = 66040.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.088354 restraints weight = 41974.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.089930 restraints weight = 32021.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.090822 restraints weight = 27120.622| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14832 Z= 0.164 Angle : 0.582 5.512 20125 Z= 0.309 Chirality : 0.045 0.255 2270 Planarity : 0.004 0.037 2568 Dihedral : 6.722 51.401 2308 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.36 % Favored : 90.19 % Rotamer: Outliers : 1.85 % Allowed : 12.22 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.19), residues: 1774 helix: -0.57 (0.40), residues: 156 sheet: -1.18 (0.26), residues: 328 loop : -1.69 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.016 0.002 TYR A 737 PHE 0.020 0.001 PHE B 404 TRP 0.005 0.001 TRP B 949 HIS 0.006 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00362 (14775) covalent geometry : angle 0.57426 (19994) SS BOND : bond 0.00234 ( 40) SS BOND : angle 0.76221 ( 80) hydrogen bonds : bond 0.03680 ( 336) hydrogen bonds : angle 7.09874 ( 876) link_NAG-ASN : bond 0.00237 ( 17) link_NAG-ASN : angle 1.90436 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 MET cc_start: 0.8904 (mmm) cc_final: 0.8372 (mmm) REVERT: E 28 MET cc_start: 0.8653 (mmm) cc_final: 0.8348 (mmm) REVERT: A 1124 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4896 (p90) REVERT: B 963 PHE cc_start: 0.6603 (t80) cc_final: 0.6369 (t80) outliers start: 30 outliers final: 22 residues processed: 108 average time/residue: 0.2302 time to fit residues: 39.5388 Evaluate side-chains 107 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.114036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.084359 restraints weight = 145138.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.087490 restraints weight = 70782.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.090147 restraints weight = 45323.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.090509 restraints weight = 37839.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.090545 restraints weight = 31769.323| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14832 Z= 0.107 Angle : 0.558 6.244 20125 Z= 0.294 Chirality : 0.045 0.257 2270 Planarity : 0.003 0.037 2568 Dihedral : 6.390 48.311 2308 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.46 % Favored : 91.09 % Rotamer: Outliers : 1.48 % Allowed : 12.84 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 1774 helix: -0.19 (0.41), residues: 156 sheet: -1.17 (0.26), residues: 328 loop : -1.57 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.012 0.001 TYR A 902 PHE 0.011 0.001 PHE B1165 TRP 0.004 0.001 TRP B 949 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00244 (14775) covalent geometry : angle 0.55120 (19994) SS BOND : bond 0.00197 ( 40) SS BOND : angle 0.62418 ( 80) hydrogen bonds : bond 0.03407 ( 336) hydrogen bonds : angle 6.80184 ( 876) link_NAG-ASN : bond 0.00206 ( 17) link_NAG-ASN : angle 1.76923 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 MET cc_start: 0.8677 (mmm) cc_final: 0.8393 (mmm) REVERT: A 384 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6735 (tt0) REVERT: A 1124 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.4812 (p90) outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 0.2303 time to fit residues: 38.0428 Evaluate side-chains 106 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.082854 restraints weight = 144178.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.086918 restraints weight = 64781.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.089530 restraints weight = 41124.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.091024 restraints weight = 31365.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.091992 restraints weight = 26720.861| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14832 Z= 0.117 Angle : 0.554 5.663 20125 Z= 0.290 Chirality : 0.044 0.249 2270 Planarity : 0.003 0.037 2568 Dihedral : 6.202 47.810 2306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.62 % Favored : 90.92 % Rotamer: Outliers : 1.48 % Allowed : 13.33 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1774 helix: -0.07 (0.42), residues: 156 sheet: -1.12 (0.26), residues: 324 loop : -1.56 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.012 0.001 TYR A 902 PHE 0.023 0.001 PHE B 404 TRP 0.003 0.001 TRP B 949 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00263 (14775) covalent geometry : angle 0.54832 (19994) SS BOND : bond 0.00189 ( 40) SS BOND : angle 0.58528 ( 80) hydrogen bonds : bond 0.03281 ( 336) hydrogen bonds : angle 6.65454 ( 876) link_NAG-ASN : bond 0.00185 ( 17) link_NAG-ASN : angle 1.68079 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 MET cc_start: 0.9053 (mmm) cc_final: 0.8809 (mmm) REVERT: E 28 MET cc_start: 0.8749 (mmm) cc_final: 0.8480 (mmm) REVERT: A 1124 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.4883 (p90) outliers start: 24 outliers final: 21 residues processed: 103 average time/residue: 0.2235 time to fit residues: 36.0469 Evaluate side-chains 106 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 50.0000 chunk 107 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.085142 restraints weight = 144503.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.088613 restraints weight = 67982.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.092523 restraints weight = 43535.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.092388 restraints weight = 33406.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.092288 restraints weight = 28823.163| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14832 Z= 0.109 Angle : 0.545 6.288 20125 Z= 0.286 Chirality : 0.044 0.244 2270 Planarity : 0.003 0.037 2568 Dihedral : 6.022 47.063 2306 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.57 % Favored : 90.92 % Rotamer: Outliers : 1.48 % Allowed : 13.77 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.20), residues: 1774 helix: 0.06 (0.42), residues: 156 sheet: -0.99 (0.27), residues: 308 loop : -1.50 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 961 TYR 0.012 0.001 TYR A 902 PHE 0.031 0.001 PHE B 963 TRP 0.003 0.001 TRP B 949 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00247 (14775) covalent geometry : angle 0.53985 (19994) SS BOND : bond 0.00166 ( 40) SS BOND : angle 0.59105 ( 80) hydrogen bonds : bond 0.03143 ( 336) hydrogen bonds : angle 6.49113 ( 876) link_NAG-ASN : bond 0.00181 ( 17) link_NAG-ASN : angle 1.61338 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 MET cc_start: 0.8684 (mmm) cc_final: 0.8423 (mmm) REVERT: A 1124 TYR cc_start: 0.5289 (OUTLIER) cc_final: 0.4907 (p90) outliers start: 24 outliers final: 23 residues processed: 103 average time/residue: 0.2352 time to fit residues: 37.8666 Evaluate side-chains 110 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 3 optimal weight: 0.0980 chunk 150 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 HIS ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** 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 = 0.4355 r_free = 0.4355 target = 0.114830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082751 restraints weight = 139285.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.087190 restraints weight = 60280.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.090004 restraints weight = 37207.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.091621 restraints weight = 27923.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.092685 restraints weight = 23610.517| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14832 Z= 0.097 Angle : 0.535 6.498 20125 Z= 0.279 Chirality : 0.044 0.242 2270 Planarity : 0.003 0.037 2568 Dihedral : 5.839 46.259 2306 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.40 % Favored : 91.09 % Rotamer: Outliers : 1.60 % Allowed : 13.58 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1774 helix: 0.25 (0.42), residues: 156 sheet: -0.95 (0.27), residues: 308 loop : -1.45 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.011 0.001 TYR A 902 PHE 0.033 0.001 PHE B 404 TRP 0.003 0.001 TRP B 949 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00222 (14775) covalent geometry : angle 0.52970 (19994) SS BOND : bond 0.00153 ( 40) SS BOND : angle 0.60456 ( 80) hydrogen bonds : bond 0.03084 ( 336) hydrogen bonds : angle 6.34919 ( 876) link_NAG-ASN : bond 0.00202 ( 17) link_NAG-ASN : angle 1.54020 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 MET cc_start: 0.8679 (mmm) cc_final: 0.8432 (mmm) REVERT: A 1124 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.4779 (p90) outliers start: 26 outliers final: 22 residues processed: 105 average time/residue: 0.2446 time to fit residues: 40.0469 Evaluate side-chains 112 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.113253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.080618 restraints weight = 139810.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.084978 restraints weight = 61612.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.087722 restraints weight = 38528.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.089384 restraints weight = 29226.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.090296 restraints weight = 24731.320| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14832 Z= 0.173 Angle : 0.563 6.774 20125 Z= 0.296 Chirality : 0.044 0.232 2270 Planarity : 0.004 0.036 2568 Dihedral : 5.943 46.468 2306 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.70 % Favored : 89.74 % Rotamer: Outliers : 1.54 % Allowed : 13.83 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.20), residues: 1774 helix: -0.11 (0.41), residues: 160 sheet: -1.08 (0.26), residues: 326 loop : -1.56 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.016 0.001 TYR A 737 PHE 0.032 0.001 PHE B 963 TRP 0.008 0.001 TRP B 522 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00384 (14775) covalent geometry : angle 0.55823 (19994) SS BOND : bond 0.00212 ( 40) SS BOND : angle 0.64404 ( 80) hydrogen bonds : bond 0.03238 ( 336) hydrogen bonds : angle 6.44742 ( 876) link_NAG-ASN : bond 0.00267 ( 17) link_NAG-ASN : angle 1.56855 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 MET cc_start: 0.8673 (mmm) cc_final: 0.8436 (mmm) REVERT: A 387 ASP cc_start: 0.7917 (m-30) cc_final: 0.7649 (m-30) REVERT: A 1124 TYR cc_start: 0.5366 (OUTLIER) cc_final: 0.5036 (p90) outliers start: 25 outliers final: 24 residues processed: 102 average time/residue: 0.2342 time to fit residues: 37.1370 Evaluate side-chains 109 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 138 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.112649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079852 restraints weight = 138497.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.084137 restraints weight = 61452.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.086892 restraints weight = 38656.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.088534 restraints weight = 29339.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.089503 restraints weight = 24836.589| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14832 Z= 0.179 Angle : 0.575 6.596 20125 Z= 0.303 Chirality : 0.045 0.233 2270 Planarity : 0.004 0.041 2568 Dihedral : 6.020 46.329 2306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.03 % Favored : 89.35 % Rotamer: Outliers : 1.42 % Allowed : 14.14 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 1774 helix: -0.29 (0.41), residues: 156 sheet: -1.22 (0.26), residues: 346 loop : -1.62 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.017 0.002 TYR A 737 PHE 0.045 0.002 PHE B 404 TRP 0.005 0.001 TRP B 949 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00393 (14775) covalent geometry : angle 0.56967 (19994) SS BOND : bond 0.00214 ( 40) SS BOND : angle 0.67472 ( 80) hydrogen bonds : bond 0.03344 ( 336) hydrogen bonds : angle 6.46202 ( 876) link_NAG-ASN : bond 0.00250 ( 17) link_NAG-ASN : angle 1.62751 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7902 (m-30) cc_final: 0.7626 (m-30) REVERT: A 1124 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.5098 (p90) REVERT: B 342 MET cc_start: 0.7060 (tpp) cc_final: 0.6773 (tpp) outliers start: 23 outliers final: 22 residues processed: 103 average time/residue: 0.2252 time to fit residues: 37.3430 Evaluate side-chains 111 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 1124 TYR Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.112864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.080049 restraints weight = 139598.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.084398 restraints weight = 61772.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.087162 restraints weight = 38808.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.088809 restraints weight = 29449.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.089540 restraints weight = 24933.468| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14832 Z= 0.164 Angle : 0.569 7.331 20125 Z= 0.298 Chirality : 0.044 0.238 2270 Planarity : 0.004 0.040 2568 Dihedral : 5.947 46.344 2306 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.92 % Favored : 89.52 % Rotamer: Outliers : 1.60 % Allowed : 14.14 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.20), residues: 1774 helix: -0.30 (0.41), residues: 156 sheet: -1.21 (0.26), residues: 346 loop : -1.64 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 438 TYR 0.015 0.002 TYR A 902 PHE 0.027 0.001 PHE B 963 TRP 0.006 0.001 TRP B 949 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00362 (14775) covalent geometry : angle 0.56290 (19994) SS BOND : bond 0.00202 ( 40) SS BOND : angle 0.64778 ( 80) hydrogen bonds : bond 0.03210 ( 336) hydrogen bonds : angle 6.41062 ( 876) link_NAG-ASN : bond 0.00243 ( 17) link_NAG-ASN : angle 1.63418 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.92 seconds wall clock time: 80 minutes 24.56 seconds (4824.56 seconds total)