Starting phenix.real_space_refine on Thu Jun 4 18:29:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hkt_52236/06_2026/9hkt_52236.map" } resolution = 3.7 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= 0.002 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 8921 2.51 5 N 2401 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14220 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6643 Classifications: {'peptide': 838} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 795} Chain breaks: 2 Chain: "B" Number of atoms: 6874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 6874 Classifications: {'peptide': 865} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 821} Chain breaks: 3 Chain: "G" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "H" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 190 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 21} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.73, per 1000 atoms: 0.26 Number of scatterers: 14220 At special positions: 0 Unit cell: (136.899, 140.773, 178.227, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 2787 8.00 N 2401 7.00 C 8921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 357 " distance=2.04 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 521 " distance=2.05 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 527 " distance=2.04 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 539 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 564 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 618 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 643 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 873 " - pdb=" SG CYS B 873 " distance=2.04 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A1258 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 521 " distance=2.04 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.04 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 643 " distance=2.04 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 664 " distance=2.04 Simple disulfide: pdb=" SG CYS B 770 " - pdb=" SG CYS B 804 " distance=2.05 Simple disulfide: pdb=" SG CYS B 981 " - pdb=" SG CYS B1258 " distance=2.04 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1188 " distance=2.03 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS G 16 " distance=2.03 Simple disulfide: pdb=" SG CYS G 12 " - pdb=" SG CYS H 3 " distance=2.04 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS H 15 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1401 " - " ASN A1147 " " NAG A1402 " - " ASN A 946 " " NAG A1403 " - " ASN A 864 " " NAG A1404 " - " ASN A 898 " " NAG A1405 " - " ASN A 356 " " NAG A1406 " - " ASN A 810 " " NAG A1407 " - " ASN A 751 " " NAG A1408 " - " ASN A 839 " " NAG A1409 " - " ASN A 569 " " NAG A1410 " - " ASN A 561 " " NAG A1411 " - " ASN A 376 " " NAG B1401 " - " ASN B 864 " " NAG B1402 " - " ASN B1147 " " NAG B1403 " - " ASN B 810 " " NAG B1404 " - " ASN B 839 " " NAG B1405 " - " ASN B 569 " " NAG B1406 " - " ASN B 751 " " NAG C 1 " - " ASN A 824 " " NAG D 1 " - " ASN B 898 " " NAG E 1 " - " ASN B 824 " " NAG F 1 " - " ASN B 946 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 690.4 milliseconds 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3316 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 37 sheets defined 11.6% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.781A pdb=" N HIS A 350 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 353 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.801A pdb=" N GLU A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.574A pdb=" N ARG A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.940A pdb=" N THR A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 removed outlier: 3.606A pdb=" N LYS A 642 " --> pdb=" O PRO A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 684 through 693 removed outlier: 3.720A pdb=" N LYS A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 removed outlier: 4.200A pdb=" N PHE A 716 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.834A pdb=" N ILE A 774 " --> pdb=" O CYS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.759A pdb=" N ASN A 798 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1205 Processing helix chain 'A' and resid 1262 through 1264 No H-bonds generated for 'chain 'A' and resid 1262 through 1264' Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.587A pdb=" N HIS B 350 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 353 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 355 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 3.648A pdb=" N GLU B 463 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 464 " --> pdb=" O TRP B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.898A pdb=" N THR B 470 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 4.150A pdb=" N ARG B 536 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 685 through 694 removed outlier: 3.783A pdb=" N TYR B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 776 through 778 No H-bonds generated for 'chain 'B' and resid 776 through 778' Processing helix chain 'B' and resid 1024 through 1044 removed outlier: 4.011A pdb=" N LYS B1028 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1124 removed outlier: 3.552A pdb=" N THR B1123 " --> pdb=" O ASP B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1178 removed outlier: 4.111A pdb=" N LEU B1178 " --> pdb=" O PRO B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1264 No H-bonds generated for 'chain 'B' and resid 1262 through 1264' Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.826A pdb=" N LEU G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.734A pdb=" N ASN H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 14 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.562A pdb=" N LEU A 364 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR A 392 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 366 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE A 389 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR A 424 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 391 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG A 446 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 422 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 448 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR A 424 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 445 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 476 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 447 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 556 removed outlier: 5.366A pdb=" N LEU A 551 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N CYS A 567 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.772A 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 585 through 586 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: 5.528A pdb=" N CYS A 647 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 723 " --> pdb=" O PHE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.097A pdb=" N LEU A 673 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N HIS A 706 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE A 675 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 760 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 736 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 808 through 809 Processing sheet with id=AB3, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.521A pdb=" N HIS A 857 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 852 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 906 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 933 through 941 removed outlier: 5.006A pdb=" N GLU A 934 " --> pdb=" O SER A 950 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 950 " --> pdb=" O GLU A 934 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 6.436A pdb=" N GLU A1127 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1140 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP A1129 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLU A1138 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 962 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 961 " --> pdb=" O CYS A1169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A1161 " --> pdb=" O ILE A 969 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A1192 " --> pdb=" O VAL A1166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1208 through 1214 removed outlier: 5.342A pdb=" N ASP A1209 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A1229 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1255 through 1260 Processing sheet with id=AB9, first strand: chain 'B' and resid 332 through 333 removed outlier: 6.773A pdb=" N LEU B 332 " --> pdb=" O CYS B 564 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 342 through 344 removed outlier: 3.523A pdb=" N LEU B 365 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 389 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR B 424 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 391 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 421 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU B 448 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 423 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 445 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR B 476 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 447 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC3, first strand: chain 'B' and resid 514 through 515 Processing sheet with id=AC4, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AC5, first strand: chain 'B' and resid 584 through 587 Processing sheet with id=AC6, first strand: chain 'B' and resid 601 through 604 Processing sheet with id=AC7, first strand: chain 'B' and resid 612 through 614 Processing sheet with id=AC8, first strand: chain 'B' and resid 626 through 627 removed outlier: 3.939A pdb=" N GLU B 636 " --> pdb=" O GLN B 627 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AD1, first strand: chain 'B' and resid 673 through 675 removed outlier: 3.575A pdb=" N TYR B 737 " --> pdb=" O LEU B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AD3, first strand: chain 'B' and resid 807 through 808 removed outlier: 5.484A pdb=" N ALA B 807 " --> pdb=" O GLU B 916 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 811 through 816 removed outlier: 6.363A pdb=" N MET B 822 " --> pdb=" O GLN B 814 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 830 through 831 removed outlier: 6.534A pdb=" N GLU B 830 " --> pdb=" O PHE B 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AD7, first strand: chain 'B' and resid 933 through 938 removed outlier: 4.776A pdb=" N GLU B 934 " --> pdb=" O SER B 950 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 950 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 6.343A pdb=" N GLU B1127 " --> pdb=" O PHE B1140 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE B1140 " --> pdb=" O GLU B1127 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B1129 " --> pdb=" O GLU B1138 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU B1138 " --> pdb=" O LEU B 968 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 961 " --> pdb=" O CYS B1169 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B1161 " --> pdb=" O ILE B 969 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1208 through 1214 removed outlier: 4.940A pdb=" N ASP B1209 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B1229 " --> pdb=" O ASP B1209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1255 through 1260 283 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3902 1.34 - 1.46: 4021 1.46 - 1.58: 6433 1.58 - 1.70: 0 1.70 - 1.83: 146 Bond restraints: 14502 Sorted by residual: bond pdb=" C PHE B 379 " pdb=" N PRO B 380 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.12e+01 bond pdb=" N GLY G 6 " pdb=" CA GLY G 6 " ideal model delta sigma weight residual 1.451 1.498 -0.047 1.60e-02 3.91e+03 8.63e+00 bond pdb=" C THR A1229 " pdb=" N PRO A1230 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.79e+00 bond pdb=" C GLU B1303 " pdb=" N PRO B1304 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.18e-02 7.18e+03 7.37e+00 bond pdb=" C PRO B1304 " pdb=" N PRO B1305 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.18e-02 7.18e+03 6.86e+00 ... (remaining 14497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 15023 1.52 - 3.03: 3736 3.03 - 4.55: 745 4.55 - 6.07: 92 6.07 - 7.59: 15 Bond angle restraints: 19611 Sorted by residual: angle pdb=" N PRO A 767 " pdb=" CA PRO A 767 " pdb=" C PRO A 767 " ideal model delta sigma weight residual 114.03 120.02 -5.99 1.23e+00 6.61e-01 2.37e+01 angle pdb=" C ASN B 925 " pdb=" CA ASN B 925 " pdb=" CB ASN B 925 " ideal model delta sigma weight residual 109.42 117.01 -7.59 1.57e+00 4.06e-01 2.33e+01 angle pdb=" N PRO A1230 " pdb=" CA PRO A1230 " pdb=" C PRO A1230 " ideal model delta sigma weight residual 110.70 116.50 -5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" C ASN A 574 " pdb=" CA ASN A 574 " pdb=" CB ASN A 574 " ideal model delta sigma weight residual 112.11 118.99 -6.88 1.46e+00 4.69e-01 2.22e+01 angle pdb=" C ASN B 970 " pdb=" N ARG B 971 " pdb=" CA ARG B 971 " ideal model delta sigma weight residual 120.39 126.73 -6.34 1.39e+00 5.18e-01 2.08e+01 ... (remaining 19606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8202 17.81 - 35.62: 879 35.62 - 53.42: 170 53.42 - 71.23: 35 71.23 - 89.04: 14 Dihedral angle restraints: 9300 sinusoidal: 4176 harmonic: 5124 Sorted by residual: dihedral pdb=" CB CYS G 25 " pdb=" SG CYS G 25 " pdb=" SG CYS H 15 " pdb=" CB CYS H 15 " ideal model delta sinusoidal sigma weight residual -86.00 -168.95 82.95 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS A 339 " pdb=" SG CYS A 339 " pdb=" SG CYS A 357 " pdb=" CB CYS A 357 " ideal model delta sinusoidal sigma weight residual 93.00 163.43 -70.43 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS B 567 " pdb=" SG CYS B 567 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual 93.00 156.27 -63.27 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 9297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1610 0.103 - 0.207: 553 0.207 - 0.310: 75 0.310 - 0.414: 5 0.414 - 0.517: 3 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.72e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.16e+01 ... (remaining 2243 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1407 " 0.335 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A1407 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1407 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1407 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1407 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.313 2.00e-02 2.50e+03 2.73e-01 9.33e+02 pdb=" C7 NAG E 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1405 " -0.319 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C7 NAG B1405 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1405 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1405 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG B1405 " -0.059 2.00e-02 2.50e+03 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6008 2.97 - 3.45: 13313 3.45 - 3.93: 23030 3.93 - 4.42: 25454 4.42 - 4.90: 41836 Nonbonded interactions: 109641 Sorted by model distance: nonbonded pdb=" OG SER B 702 " pdb=" O PRO B 727 " model vdw 2.486 3.040 nonbonded pdb=" OH TYR A 709 " pdb=" OD2 ASP B1026 " model vdw 2.493 3.040 nonbonded pdb=" O ARG A 411 " pdb=" OG1 THR A 441 " model vdw 2.501 3.040 nonbonded pdb=" O LYS B 758 " pdb=" N GLY B 760 " model vdw 2.503 3.120 nonbonded pdb=" OG SER A 701 " pdb=" N SER A 702 " model vdw 2.520 3.120 ... (remaining 109636 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 330 through 1406) selection = (chain 'B' and (resid 330 through 493 or resid 510 through 1023 or resid 1118 th \ rough 1406)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.830 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.007 0.047 14565 Z= 0.470 Angle : 1.393 8.340 19762 Z= 0.904 Chirality : 0.098 0.517 2246 Planarity : 0.019 0.287 2513 Dihedral : 15.138 89.038 5870 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.46 % Allowed : 7.07 % Favored : 90.47 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.17), residues: 1730 helix: -3.27 (0.33), residues: 129 sheet: -1.57 (0.24), residues: 385 loop : -2.10 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 657 TYR 0.020 0.002 TYR A 388 PHE 0.021 0.003 PHE A 855 TRP 0.013 0.002 TRP A 461 HIS 0.006 0.001 HIS B 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.47 (14502) covalent geometry : angle 1.38636 / 0.91 (19611) SS BOND : bond 0.00770 / 0.46 ( 38) SS BOND : angle 1.12730 / 0.76 ( 76) hydrogen bonds : bond 0.22658 / 15.28 ( 283) hydrogen bonds : angle 9.35533 / 6.31 ( 705) link_BETA1-4 : bond 0.00809 / 0.40 ( 4) link_BETA1-4 : angle 2.60723 / 1.42 ( 12) link_NAG-ASN : bond 0.00574 / 0.38 ( 21) link_NAG-ASN : angle 2.75773 / 1.81 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 0.631 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: A 359 VAL cc_start: 0.9000 (t) cc_final: 0.8698 (p) REVERT: A 369 ILE cc_start: 0.8915 (mm) cc_final: 0.8692 (mm) REVERT: A 406 ASN cc_start: 0.7617 (t0) cc_final: 0.7409 (t0) REVERT: A 448 GLU cc_start: 0.7788 (tt0) cc_final: 0.7519 (tt0) REVERT: A 481 GLU cc_start: 0.7686 (tt0) cc_final: 0.7382 (tp30) REVERT: A 519 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.6932 (ttm110) REVERT: A 548 GLN cc_start: 0.8044 (mt0) cc_final: 0.7726 (mm-40) REVERT: A 572 PHE cc_start: 0.7807 (t80) cc_final: 0.7359 (t80) REVERT: A 604 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6913 (tp30) REVERT: A 614 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.5369 (t80) REVERT: A 620 THR cc_start: 0.9006 (p) cc_final: 0.8792 (p) REVERT: A 674 THR cc_start: 0.9004 (m) cc_final: 0.8400 (p) REVERT: A 713 SER cc_start: 0.9211 (p) cc_final: 0.8986 (p) REVERT: A 754 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (m) REVERT: A 792 ASP cc_start: 0.7458 (m-30) cc_final: 0.7225 (m-30) REVERT: A 859 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8220 (pt) REVERT: A 919 VAL cc_start: 0.8676 (t) cc_final: 0.8462 (p) REVERT: A 967 LYS cc_start: 0.7839 (mttt) cc_final: 0.7580 (mptt) REVERT: A 1159 PHE cc_start: 0.5247 (t80) cc_final: 0.4646 (t80) REVERT: A 1170 ARG cc_start: 0.5609 (ptt90) cc_final: 0.5394 (ptt90) REVERT: B 342 MET cc_start: 0.1199 (mtt) cc_final: 0.0593 (ttp) REVERT: B 403 ILE cc_start: -0.0774 (OUTLIER) cc_final: -0.1207 (mt) REVERT: B 430 MET cc_start: 0.3285 (mtt) cc_final: 0.2523 (ptt) REVERT: B 645 LYS cc_start: 0.7298 (pttt) cc_final: 0.7072 (pttm) REVERT: B 651 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8608 (tt) REVERT: B 686 MET cc_start: 0.8890 (mtp) cc_final: 0.8681 (mtm) REVERT: B 687 ASP cc_start: 0.7520 (t70) cc_final: 0.7257 (m-30) REVERT: B 724 SER cc_start: 0.6666 (OUTLIER) cc_final: 0.6438 (t) REVERT: B 742 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6944 (ttm-80) REVERT: B 746 GLU cc_start: 0.8300 (tt0) cc_final: 0.7972 (tp30) REVERT: B 761 VAL cc_start: 0.8608 (p) cc_final: 0.8351 (p) REVERT: B 797 SER cc_start: 0.8427 (m) cc_final: 0.7947 (p) REVERT: B 813 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6842 (pt) REVERT: B 845 LYS cc_start: 0.8054 (mttt) cc_final: 0.7705 (mttt) REVERT: B 876 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7586 (ttp-110) REVERT: B 903 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 931 LYS cc_start: 0.7107 (pttt) cc_final: 0.6756 (mttp) REVERT: B 1137 TYR cc_start: 0.7962 (m-80) cc_final: 0.7673 (m-80) REVERT: B 1164 ILE cc_start: 0.8836 (mt) cc_final: 0.8431 (tp) REVERT: B 1171 GLU cc_start: 0.8271 (mt-10) cc_final: 0.6834 (pm20) REVERT: G 9 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7381 (tp30) REVERT: H 6 LYS cc_start: 0.7756 (mptt) cc_final: 0.7484 (mtpt) REVERT: H 18 TYR cc_start: 0.7570 (m-80) cc_final: 0.7305 (m-80) REVERT: H 22 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8615 (pt) outliers start: 39 outliers final: 11 residues processed: 299 average time/residue: 0.1437 time to fit residues: 60.6176 Evaluate side-chains 194 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain H residue 22 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 586 GLN A 615 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 HIS A 775 ASN A 991 ASN A1235 ASN B 764 HIS B 857 HIS B1218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.215015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.203922 restraints weight = 20329.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.203017 restraints weight = 48766.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.202416 restraints weight = 47911.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.200825 restraints weight = 42192.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.200329 restraints weight = 48347.718| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14565 Z= 0.175 Angle : 0.717 12.318 19762 Z= 0.373 Chirality : 0.048 0.197 2246 Planarity : 0.004 0.049 2513 Dihedral : 8.288 57.243 2450 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 3.15 % Allowed : 11.17 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.18), residues: 1730 helix: -2.91 (0.35), residues: 146 sheet: -1.29 (0.24), residues: 391 loop : -1.66 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 961 TYR 0.019 0.002 TYR A 899 PHE 0.026 0.002 PHE B 963 TRP 0.010 0.001 TRP B 522 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (14502) covalent geometry : angle 0.69240 / 0.36 (19611) SS BOND : bond 0.00387 / 0.22 ( 38) SS BOND : angle 2.40122 / 1.45 ( 76) hydrogen bonds : bond 0.04928 / 3.23 ( 283) hydrogen bonds : angle 6.93137 / 4.68 ( 705) link_BETA1-4 : bond 0.00435 / 0.22 ( 4) link_BETA1-4 : angle 1.94684 / 0.95 ( 12) link_NAG-ASN : bond 0.00295 / 0.19 ( 21) link_NAG-ASN : angle 2.09904 / 1.37 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7863 (t0) cc_final: 0.7293 (t0) REVERT: A 406 ASN cc_start: 0.7604 (t0) cc_final: 0.6956 (t0) REVERT: A 614 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.3998 (t80) REVERT: A 653 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7328 (t0) REVERT: A 792 ASP cc_start: 0.7287 (m-30) cc_final: 0.6882 (m-30) REVERT: A 859 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8023 (pt) REVERT: A 888 MET cc_start: 0.5938 (tpt) cc_final: 0.4826 (tpp) REVERT: B 430 MET cc_start: 0.2412 (mtt) cc_final: 0.1371 (ptt) REVERT: B 709 TYR cc_start: 0.5889 (m-10) cc_final: 0.5562 (m-80) REVERT: B 724 SER cc_start: 0.6749 (OUTLIER) cc_final: 0.6488 (t) REVERT: B 822 MET cc_start: 0.6405 (tmm) cc_final: 0.6186 (tmm) REVERT: B 1136 PHE cc_start: 0.5324 (p90) cc_final: 0.4946 (p90) REVERT: H 13 MET cc_start: 0.5715 (ptt) cc_final: 0.5506 (ptt) outliers start: 50 outliers final: 26 residues processed: 219 average time/residue: 0.1405 time to fit residues: 43.2015 Evaluate side-chains 159 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1202 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 96 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.212637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.201545 restraints weight = 20795.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.199889 restraints weight = 49361.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.199022 restraints weight = 51685.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.192890 restraints weight = 47194.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.189679 restraints weight = 44137.178| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14565 Z= 0.206 Angle : 0.694 11.842 19762 Z= 0.359 Chirality : 0.048 0.212 2246 Planarity : 0.004 0.052 2513 Dihedral : 7.379 56.304 2437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.97 % Allowed : 13.50 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.19), residues: 1730 helix: -2.55 (0.39), residues: 136 sheet: -1.18 (0.25), residues: 388 loop : -1.48 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 971 TYR 0.020 0.002 TYR A 614 PHE 0.025 0.002 PHE B1151 TRP 0.008 0.001 TRP B 748 HIS 0.004 0.001 HIS B 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (14502) covalent geometry : angle 0.67941 / 0.35 (19611) SS BOND : bond 0.00462 / 0.29 ( 38) SS BOND : angle 1.58708 / 1.10 ( 76) hydrogen bonds : bond 0.04530 / 2.93 ( 283) hydrogen bonds : angle 6.61061 / 4.45 ( 705) link_BETA1-4 : bond 0.00330 / 0.17 ( 4) link_BETA1-4 : angle 2.34536 / 1.19 ( 12) link_NAG-ASN : bond 0.00223 / 0.14 ( 21) link_NAG-ASN : angle 1.76413 / 1.17 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7514 (mmt) REVERT: A 343 ASP cc_start: 0.7743 (t0) cc_final: 0.7363 (t0) REVERT: A 369 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 406 ASN cc_start: 0.7564 (t0) cc_final: 0.7056 (t0) REVERT: A 614 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.4266 (t80) REVERT: A 705 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7597 (m) REVERT: A 754 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8020 (p) REVERT: A 859 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7979 (pt) REVERT: A 1159 PHE cc_start: 0.4625 (t80) cc_final: 0.4178 (t80) REVERT: B 430 MET cc_start: 0.2848 (mtt) cc_final: 0.1676 (ptt) REVERT: B 709 TYR cc_start: 0.6154 (m-10) cc_final: 0.5896 (m-80) REVERT: B 724 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6370 (p) REVERT: B 732 ASP cc_start: 0.6460 (t0) cc_final: 0.5953 (t0) REVERT: B 742 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7237 (ttm-80) REVERT: B 1136 PHE cc_start: 0.6416 (p90) cc_final: 0.5908 (p90) outliers start: 63 outliers final: 41 residues processed: 185 average time/residue: 0.1201 time to fit residues: 33.1741 Evaluate side-chains 176 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1121 GLU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 129 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN B1150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.214365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.203114 restraints weight = 20745.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.202171 restraints weight = 48631.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.201210 restraints weight = 47418.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.200255 restraints weight = 48486.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.199883 restraints weight = 46182.372| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14565 Z= 0.142 Angle : 0.612 13.091 19762 Z= 0.314 Chirality : 0.047 0.191 2246 Planarity : 0.004 0.073 2513 Dihedral : 6.840 58.506 2437 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.28 % Allowed : 15.33 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1730 helix: -2.20 (0.42), residues: 136 sheet: -1.00 (0.26), residues: 384 loop : -1.30 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1284 TYR 0.024 0.002 TYR B1245 PHE 0.026 0.002 PHE B1151 TRP 0.009 0.001 TRP B 522 HIS 0.002 0.001 HIS B 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14502) covalent geometry : angle 0.59981 / 0.31 (19611) SS BOND : bond 0.00328 / 0.22 ( 38) SS BOND : angle 1.25993 / 0.86 ( 76) hydrogen bonds : bond 0.03674 / 2.40 ( 283) hydrogen bonds : angle 6.37815 / 4.32 ( 705) link_BETA1-4 : bond 0.00272 / 0.13 ( 4) link_BETA1-4 : angle 2.06711 / 1.09 ( 12) link_NAG-ASN : bond 0.00179 / 0.11 ( 21) link_NAG-ASN : angle 1.68085 / 1.13 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7515 (mmt) REVERT: A 343 ASP cc_start: 0.7727 (t0) cc_final: 0.7467 (t0) REVERT: A 369 ILE cc_start: 0.8745 (mm) cc_final: 0.8488 (mt) REVERT: A 387 ASP cc_start: 0.7485 (t0) cc_final: 0.7105 (t0) REVERT: A 614 TYR cc_start: 0.5644 (OUTLIER) cc_final: 0.4189 (t80) REVERT: A 653 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7687 (t0) REVERT: A 686 MET cc_start: 0.8514 (mmm) cc_final: 0.8048 (mmp) REVERT: A 704 MET cc_start: 0.7598 (ttp) cc_final: 0.7282 (ptm) REVERT: A 705 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7403 (t) REVERT: A 754 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 859 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 430 MET cc_start: 0.2391 (mtt) cc_final: 0.1420 (ptt) REVERT: B 691 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6401 (t80) REVERT: B 724 SER cc_start: 0.6957 (OUTLIER) cc_final: 0.6473 (p) REVERT: B 732 ASP cc_start: 0.6009 (t0) cc_final: 0.5550 (t0) REVERT: B 1136 PHE cc_start: 0.5780 (p90) cc_final: 0.5489 (p90) outliers start: 52 outliers final: 30 residues processed: 174 average time/residue: 0.1108 time to fit residues: 29.6971 Evaluate side-chains 160 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 167 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A 977 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.213404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.201777 restraints weight = 20580.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.200720 restraints weight = 51433.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.198182 restraints weight = 50227.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.195477 restraints weight = 49483.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.194733 restraints weight = 43370.614| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14565 Z= 0.169 Angle : 0.628 14.320 19762 Z= 0.322 Chirality : 0.047 0.213 2246 Planarity : 0.004 0.046 2513 Dihedral : 6.667 55.945 2435 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.10 % Allowed : 15.84 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.19), residues: 1730 helix: -2.13 (0.42), residues: 135 sheet: -1.05 (0.25), residues: 389 loop : -1.30 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1200 TYR 0.020 0.002 TYR A 614 PHE 0.017 0.002 PHE A 922 TRP 0.008 0.001 TRP B 522 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (14502) covalent geometry : angle 0.61623 / 0.32 (19611) SS BOND : bond 0.00318 / 0.21 ( 38) SS BOND : angle 1.27041 / 0.79 ( 76) hydrogen bonds : bond 0.03652 / 2.40 ( 283) hydrogen bonds : angle 6.34901 / 4.31 ( 705) link_BETA1-4 : bond 0.00319 / 0.15 ( 4) link_BETA1-4 : angle 2.08184 / 1.06 ( 12) link_NAG-ASN : bond 0.00200 / 0.12 ( 21) link_NAG-ASN : angle 1.69304 / 1.14 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7750 (t0) cc_final: 0.7409 (t0) REVERT: A 614 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.3943 (t80) REVERT: A 653 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7909 (t0) REVERT: A 704 MET cc_start: 0.7620 (ttp) cc_final: 0.7371 (ptm) REVERT: A 705 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7301 (t) REVERT: A 754 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 859 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8120 (pt) REVERT: B 430 MET cc_start: 0.2633 (mtt) cc_final: 0.1504 (ptt) REVERT: B 691 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6361 (t80) REVERT: B 724 SER cc_start: 0.7021 (OUTLIER) cc_final: 0.6626 (t) REVERT: B 732 ASP cc_start: 0.6022 (t0) cc_final: 0.5544 (t0) REVERT: B 960 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.6935 (m) REVERT: H 5 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6994 (tm-30) outliers start: 65 outliers final: 44 residues processed: 178 average time/residue: 0.1164 time to fit residues: 31.6199 Evaluate side-chains 173 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 49 optimal weight: 0.2980 chunk 136 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 170 optimal weight: 0.0980 chunk 160 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.4565 r_free = 0.4565 target = 0.215061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.203739 restraints weight = 20559.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.202400 restraints weight = 49183.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.200309 restraints weight = 52369.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.197777 restraints weight = 51247.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.197117 restraints weight = 41476.745| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14565 Z= 0.130 Angle : 0.595 13.479 19762 Z= 0.303 Chirality : 0.046 0.206 2246 Planarity : 0.004 0.050 2513 Dihedral : 6.317 48.765 2435 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.60 % Allowed : 16.97 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1730 helix: -1.91 (0.43), residues: 135 sheet: -0.95 (0.26), residues: 386 loop : -1.19 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 848 TYR 0.017 0.001 TYR A 614 PHE 0.029 0.002 PHE B1136 TRP 0.008 0.001 TRP B 522 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14502) covalent geometry : angle 0.58418 / 0.30 (19611) SS BOND : bond 0.00383 / 0.20 ( 38) SS BOND : angle 1.06346 / 0.66 ( 76) hydrogen bonds : bond 0.03276 / 2.17 ( 283) hydrogen bonds : angle 6.18684 / 4.22 ( 705) link_BETA1-4 : bond 0.00277 / 0.13 ( 4) link_BETA1-4 : angle 1.98161 / 1.03 ( 12) link_NAG-ASN : bond 0.00180 / 0.11 ( 21) link_NAG-ASN : angle 1.62574 / 1.10 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.3955 (t80) REVERT: A 653 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 686 MET cc_start: 0.8561 (mmm) cc_final: 0.8237 (mmp) REVERT: A 704 MET cc_start: 0.7540 (ttp) cc_final: 0.7310 (ptm) REVERT: A 754 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 788 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: A 859 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8085 (pt) REVERT: A 1160 THR cc_start: 0.3704 (OUTLIER) cc_final: 0.3311 (m) REVERT: B 430 MET cc_start: 0.2632 (mtt) cc_final: 0.1490 (ptt) REVERT: B 691 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6247 (t80) REVERT: B 724 SER cc_start: 0.6923 (OUTLIER) cc_final: 0.6620 (t) REVERT: B 732 ASP cc_start: 0.5862 (t0) cc_final: 0.5372 (t0) REVERT: B 960 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7026 (m) REVERT: H 5 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7057 (tm-30) outliers start: 57 outliers final: 36 residues processed: 171 average time/residue: 0.1151 time to fit residues: 30.2849 Evaluate side-chains 165 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 chunk 90 optimal weight: 30.0000 chunk 150 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS B 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.212927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.200381 restraints weight = 20519.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.199031 restraints weight = 51242.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.198316 restraints weight = 48534.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.197234 restraints weight = 48041.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.196908 restraints weight = 49503.637| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14565 Z= 0.201 Angle : 0.647 13.398 19762 Z= 0.329 Chirality : 0.048 0.231 2246 Planarity : 0.004 0.045 2513 Dihedral : 6.351 49.635 2432 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.35 % Allowed : 16.53 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.20), residues: 1730 helix: -2.02 (0.42), residues: 135 sheet: -1.14 (0.26), residues: 378 loop : -1.18 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 536 TYR 0.021 0.002 TYR A 614 PHE 0.027 0.002 PHE B1151 TRP 0.008 0.001 TRP B 522 HIS 0.004 0.001 HIS B 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (14502) covalent geometry : angle 0.63537 / 0.33 (19611) SS BOND : bond 0.00380 / 0.23 ( 38) SS BOND : angle 1.30001 / 0.83 ( 76) hydrogen bonds : bond 0.03629 / 2.40 ( 283) hydrogen bonds : angle 6.36176 / 4.34 ( 705) link_BETA1-4 : bond 0.00303 / 0.14 ( 4) link_BETA1-4 : angle 2.03325 / 1.03 ( 12) link_NAG-ASN : bond 0.00189 / 0.11 ( 21) link_NAG-ASN : angle 1.67488 / 1.12 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 123 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ILE cc_start: 0.8810 (mm) cc_final: 0.8572 (mt) REVERT: A 614 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.4067 (t80) REVERT: A 653 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 754 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 788 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: B 430 MET cc_start: 0.2517 (mtt) cc_final: 0.1349 (ptt) REVERT: B 612 ILE cc_start: -0.2881 (OUTLIER) cc_final: -0.3197 (mp) REVERT: B 691 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6279 (t80) REVERT: B 724 SER cc_start: 0.6877 (OUTLIER) cc_final: 0.6545 (t) REVERT: B 732 ASP cc_start: 0.5809 (t0) cc_final: 0.5308 (t0) REVERT: B 960 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7111 (m) REVERT: H 5 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7069 (tm-30) outliers start: 69 outliers final: 50 residues processed: 174 average time/residue: 0.1113 time to fit residues: 29.8380 Evaluate side-chains 176 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN B1266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.213331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.200677 restraints weight = 20542.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.199354 restraints weight = 48546.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.198646 restraints weight = 50591.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.194473 restraints weight = 46520.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.192026 restraints weight = 35362.018| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14565 Z= 0.175 Angle : 0.630 13.845 19762 Z= 0.320 Chirality : 0.047 0.226 2246 Planarity : 0.004 0.045 2513 Dihedral : 6.237 49.638 2430 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.35 % Allowed : 16.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.20), residues: 1730 helix: -2.11 (0.41), residues: 143 sheet: -1.13 (0.26), residues: 379 loop : -1.16 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 411 TYR 0.020 0.002 TYR A 614 PHE 0.026 0.002 PHE B1151 TRP 0.008 0.001 TRP B 522 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (14502) covalent geometry : angle 0.61973 / 0.32 (19611) SS BOND : bond 0.00360 / 0.22 ( 38) SS BOND : angle 1.08683 / 0.70 ( 76) hydrogen bonds : bond 0.03439 / 2.27 ( 283) hydrogen bonds : angle 6.31877 / 4.31 ( 705) link_BETA1-4 : bond 0.00265 / 0.13 ( 4) link_BETA1-4 : angle 1.95736 / 0.99 ( 12) link_NAG-ASN : bond 0.00190 / 0.11 ( 21) link_NAG-ASN : angle 1.63885 / 1.09 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 120 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.7080 (mtp-110) REVERT: A 614 TYR cc_start: 0.5831 (OUTLIER) cc_final: 0.4044 (t80) REVERT: A 653 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 788 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: A 859 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8156 (pt) REVERT: A 888 MET cc_start: 0.6376 (tpt) cc_final: 0.5054 (tpp) REVERT: B 430 MET cc_start: 0.3487 (mtt) cc_final: 0.2387 (ptt) REVERT: B 612 ILE cc_start: -0.2851 (OUTLIER) cc_final: -0.3173 (mp) REVERT: B 691 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6236 (t80) REVERT: B 724 SER cc_start: 0.6836 (OUTLIER) cc_final: 0.6547 (t) REVERT: B 732 ASP cc_start: 0.5836 (t0) cc_final: 0.5336 (t0) REVERT: B 888 MET cc_start: 0.7678 (tpp) cc_final: 0.6709 (tpp) REVERT: B 960 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7269 (m) REVERT: H 5 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7029 (tm-30) outliers start: 69 outliers final: 54 residues processed: 171 average time/residue: 0.1125 time to fit residues: 29.8435 Evaluate side-chains 176 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 114 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1121 GLU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 158 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN ** A 741 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 = 0.4561 r_free = 0.4561 target = 0.214694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.203028 restraints weight = 20616.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.202410 restraints weight = 50131.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201714 restraints weight = 48927.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.200316 restraints weight = 42679.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.199946 restraints weight = 44013.712| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14565 Z= 0.126 Angle : 0.588 14.142 19762 Z= 0.298 Chirality : 0.046 0.209 2246 Planarity : 0.004 0.044 2513 Dihedral : 5.908 50.964 2430 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.72 % Allowed : 17.03 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1730 helix: -1.96 (0.42), residues: 143 sheet: -1.02 (0.26), residues: 377 loop : -1.09 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.017 0.001 TYR A 614 PHE 0.021 0.002 PHE B1151 TRP 0.007 0.001 TRP B 522 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14502) covalent geometry : angle 0.57913 / 0.30 (19611) SS BOND : bond 0.00268 / 0.16 ( 38) SS BOND : angle 0.87383 / 0.57 ( 76) hydrogen bonds : bond 0.03068 / 2.04 ( 283) hydrogen bonds : angle 6.11548 / 4.18 ( 705) link_BETA1-4 : bond 0.00356 / 0.17 ( 4) link_BETA1-4 : angle 1.83999 / 0.94 ( 12) link_NAG-ASN : bond 0.00168 / 0.11 ( 21) link_NAG-ASN : angle 1.58040 / 1.06 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ARG cc_start: 0.7314 (mtp-110) cc_final: 0.7036 (mtp-110) REVERT: A 614 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.3994 (t80) REVERT: A 653 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7376 (t0) REVERT: A 788 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7157 (m-10) REVERT: A 888 MET cc_start: 0.6198 (tpt) cc_final: 0.4902 (tpp) REVERT: A 1160 THR cc_start: 0.3223 (OUTLIER) cc_final: 0.2898 (m) REVERT: B 430 MET cc_start: 0.3179 (mtt) cc_final: 0.2068 (ptt) REVERT: B 612 ILE cc_start: -0.2823 (OUTLIER) cc_final: -0.3152 (mp) REVERT: B 691 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6179 (t80) REVERT: B 724 SER cc_start: 0.6901 (OUTLIER) cc_final: 0.6671 (t) REVERT: B 732 ASP cc_start: 0.5622 (t0) cc_final: 0.5107 (t0) REVERT: B 960 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6767 (m) REVERT: H 5 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7057 (tm-30) outliers start: 59 outliers final: 45 residues processed: 166 average time/residue: 0.1145 time to fit residues: 28.9555 Evaluate side-chains 169 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.4544 r_free = 0.4544 target = 0.212926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.201721 restraints weight = 20485.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.200531 restraints weight = 46383.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.199752 restraints weight = 48448.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.193367 restraints weight = 46736.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.189690 restraints weight = 37293.530| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14565 Z= 0.190 Angle : 0.636 14.167 19762 Z= 0.322 Chirality : 0.048 0.226 2246 Planarity : 0.004 0.044 2513 Dihedral : 6.002 51.258 2428 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.72 % Allowed : 16.97 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1730 helix: -2.08 (0.41), residues: 143 sheet: -1.08 (0.26), residues: 383 loop : -1.12 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1284 TYR 0.021 0.002 TYR A 614 PHE 0.026 0.002 PHE A 572 TRP 0.009 0.001 TRP B 877 HIS 0.004 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (14502) covalent geometry : angle 0.62634 / 0.32 (19611) SS BOND : bond 0.00347 / 0.21 ( 38) SS BOND : angle 1.08897 / 0.70 ( 76) hydrogen bonds : bond 0.03458 / 2.29 ( 283) hydrogen bonds : angle 6.25570 / 4.27 ( 705) link_BETA1-4 : bond 0.00301 / 0.14 ( 4) link_BETA1-4 : angle 1.90981 / 0.94 ( 12) link_NAG-ASN : bond 0.00182 / 0.11 ( 21) link_NAG-ASN : angle 1.57305 / 1.04 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ILE cc_start: 0.8840 (mm) cc_final: 0.8624 (mt) REVERT: A 614 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.4277 (t80) REVERT: A 653 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7594 (t0) REVERT: A 660 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 788 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7034 (m-10) REVERT: A 859 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8205 (pt) REVERT: A 888 MET cc_start: 0.6398 (tpt) cc_final: 0.5358 (tpp) REVERT: A 922 PHE cc_start: 0.7283 (p90) cc_final: 0.6744 (p90) REVERT: A 1160 THR cc_start: 0.4059 (OUTLIER) cc_final: 0.3581 (m) REVERT: B 430 MET cc_start: 0.3812 (mtt) cc_final: 0.2531 (ptt) REVERT: B 612 ILE cc_start: -0.2767 (OUTLIER) cc_final: -0.3092 (mp) REVERT: B 691 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6317 (t80) REVERT: B 732 ASP cc_start: 0.5846 (t0) cc_final: 0.5292 (t0) REVERT: B 888 MET cc_start: 0.7698 (tpp) cc_final: 0.6692 (tpp) REVERT: B 960 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7154 (m) REVERT: H 5 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7137 (tm-30) outliers start: 59 outliers final: 47 residues processed: 166 average time/residue: 0.1138 time to fit residues: 29.2001 Evaluate side-chains 175 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 923 ARG Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1121 GLU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain G residue 14 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 126 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.4555 r_free = 0.4555 target = 0.214032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.202818 restraints weight = 20539.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.201946 restraints weight = 45654.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.200727 restraints weight = 42609.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191830 restraints weight = 38111.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185918 restraints weight = 29031.443| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14565 Z= 0.147 Angle : 0.606 14.511 19762 Z= 0.306 Chirality : 0.046 0.213 2246 Planarity : 0.004 0.044 2513 Dihedral : 5.819 52.152 2427 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.72 % Allowed : 17.03 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1730 helix: -1.96 (0.42), residues: 143 sheet: -1.02 (0.26), residues: 383 loop : -1.08 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 848 TYR 0.018 0.001 TYR A 614 PHE 0.023 0.002 PHE A 603 TRP 0.008 0.001 TRP B 522 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14502) covalent geometry : angle 0.59771 / 0.30 (19611) SS BOND : bond 0.00309 / 0.18 ( 38) SS BOND : angle 0.90744 / 0.59 ( 76) hydrogen bonds : bond 0.03162 / 2.09 ( 283) hydrogen bonds : angle 6.11696 / 4.18 ( 705) link_BETA1-4 : bond 0.00303 / 0.15 ( 4) link_BETA1-4 : angle 1.80244 / 0.90 ( 12) link_NAG-ASN : bond 0.00173 / 0.11 ( 21) link_NAG-ASN : angle 1.52480 / 1.00 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.63 seconds wall clock time: 39 minutes 47.63 seconds (2387.63 seconds total)