Starting phenix.real_space_refine on Tue Jun 17 06:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyo_41727/06_2025/8tyo_41727.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 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 78 5.16 5 C 12401 2.51 5 N 3198 2.21 5 O 3781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19458 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6104 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 749} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5824 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 717} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7124 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 42, 'TRANS': 870} Chain breaks: 10 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.64, per 1000 atoms: 0.60 Number of scatterers: 19458 At special positions: 0 Unit cell: (132.24, 129.92, 162.4, 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 78 16.00 O 3781 8.00 N 3198 7.00 C 12401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C1098 " " NAG D 1 " - " ASN C 717 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.4 seconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 28.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.724A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.537A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 991 through 1032 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.562A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.123A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.883A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.093A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.827A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.991A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.134A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.504A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.838A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.816A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.631A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.932A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.638A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.664A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.865A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.757A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.394A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.005A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.864A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.555A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.841A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.806A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.065A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.375A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.556A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.677A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.964A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.596A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.019A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 864 hydrogen bonds defined for protein. 2418 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: 7.77 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6204 1.35 - 1.47: 4911 1.47 - 1.59: 8630 1.59 - 1.71: 0 1.71 - 1.84: 102 Bond restraints: 19847 Sorted by residual: bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.43e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 19842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 26377 1.51 - 3.02: 544 3.02 - 4.52: 49 4.52 - 6.03: 8 6.03 - 7.54: 7 Bond angle restraints: 26985 Sorted by residual: angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA PRO C 225 " pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 112.00 108.22 3.78 1.40e+00 5.10e-01 7.29e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 113.93 -3.23 1.22e+00 6.72e-01 7.00e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 113.85 -3.15 1.22e+00 6.72e-01 6.67e+00 angle pdb=" N GLY B 283 " pdb=" CA GLY B 283 " pdb=" C GLY B 283 " ideal model delta sigma weight residual 113.18 119.19 -6.01 2.37e+00 1.78e-01 6.44e+00 ... (remaining 26980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 11380 21.28 - 42.56: 681 42.56 - 63.84: 104 63.84 - 85.12: 25 85.12 - 106.40: 13 Dihedral angle restraints: 12203 sinusoidal: 5099 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.26 84.26 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -144.48 58.48 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -37.66 -48.34 1 1.00e+01 1.00e-02 3.22e+01 ... (remaining 12200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2415 0.044 - 0.088: 533 0.088 - 0.132: 265 0.132 - 0.176: 10 0.176 - 0.220: 2 Chirality restraints: 3225 Sorted by residual: chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 3222 not shown) Planarity restraints: 3452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 225 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " 0.055 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 621 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.015 2.00e-02 2.50e+03 1.47e-02 3.80e+00 pdb=" CG PHE A 906 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 3449 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 218 2.66 - 3.22: 17237 3.22 - 3.78: 28483 3.78 - 4.34: 40424 4.34 - 4.90: 68577 Nonbonded interactions: 154939 Sorted by model distance: nonbonded pdb=" OG SER C 605 " pdb=" OE1 GLN C 607 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.190 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.237 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.241 3.040 ... (remaining 154934 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 27 through 65 or resid 88 through 107 or resid 116 through \ 122 or resid 124 through 130 or resid 168 through 172 or resid 189 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 330 or resid 531 through 620 or resid 641 through 676 or resid 690 t \ hrough 1140 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 130 or resid 168 through 676 or resid 690 throu \ gh 1140 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 65 or resid 88 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 107 or resi \ d 116 through 122 or resid 124 through 196 or (resid 197 and (name N or name CA \ or name C or name O or name CB )) or resid 198 through 330 or resid 531 through \ 811 or resid 813 through 1140 or resid 1301 through 1309)) } 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 individual isotropic 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.180 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19902 Z= 0.154 Angle : 0.523 7.540 27123 Z= 0.267 Chirality : 0.044 0.220 3225 Planarity : 0.004 0.117 3425 Dihedral : 13.935 106.400 7532 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2383 helix: 2.60 (0.21), residues: 593 sheet: 0.84 (0.21), residues: 550 loop : -0.79 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.034 0.001 PHE A 906 TYR 0.017 0.001 TYR C 369 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 27) link_NAG-ASN : angle 1.47854 ( 81) link_BETA1-4 : bond 0.00313 ( 1) link_BETA1-4 : angle 0.90441 ( 3) hydrogen bonds : bond 0.14121 ( 864) hydrogen bonds : angle 6.55190 ( 2418) SS BOND : bond 0.00384 ( 27) SS BOND : angle 1.37527 ( 54) covalent geometry : bond 0.00343 (19847) covalent geometry : angle 0.51472 (26985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7550 (m-30) cc_final: 0.7325 (m-30) REVERT: A 544 ASN cc_start: 0.7342 (m110) cc_final: 0.7010 (m-40) REVERT: A 856 ASN cc_start: 0.7485 (m110) cc_final: 0.7117 (m110) REVERT: A 902 MET cc_start: 0.8502 (mmp) cc_final: 0.8054 (mmt) REVERT: A 1138 TYR cc_start: 0.7073 (m-80) cc_final: 0.6805 (m-80) REVERT: B 282 ASN cc_start: 0.6525 (m-40) cc_final: 0.5542 (t0) REVERT: B 558 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7328 (mmmm) REVERT: B 1010 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7194 (pt0) REVERT: C 658 ASN cc_start: 0.7195 (m110) cc_final: 0.6950 (m-40) REVERT: C 773 GLU cc_start: 0.7656 (tt0) cc_final: 0.7442 (tt0) REVERT: C 921 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7670 (mttp) REVERT: C 1050 MET cc_start: 0.8356 (ptp) cc_final: 0.8152 (ptm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 1.2663 time to fit residues: 328.2433 Evaluate side-chains 163 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 221 optimal weight: 3.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 901 GLN A 955 ASN A1101 HIS B 901 GLN C 87 ASN C 564 GLN C 804 GLN C 856 ASN C 901 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.195030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143461 restraints weight = 21361.454| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.10 r_work: 0.3570 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19902 Z= 0.113 Angle : 0.509 8.363 27123 Z= 0.267 Chirality : 0.044 0.190 3225 Planarity : 0.004 0.073 3425 Dihedral : 7.255 69.777 3201 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.12 % Allowed : 7.11 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2383 helix: 2.81 (0.21), residues: 605 sheet: 0.96 (0.21), residues: 566 loop : -0.80 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.021 0.001 PHE A 906 TYR 0.019 0.001 TYR C 904 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 27) link_NAG-ASN : angle 1.58573 ( 81) link_BETA1-4 : bond 0.00170 ( 1) link_BETA1-4 : angle 1.21904 ( 3) hydrogen bonds : bond 0.04311 ( 864) hydrogen bonds : angle 5.25844 ( 2418) SS BOND : bond 0.00373 ( 27) SS BOND : angle 1.14267 ( 54) covalent geometry : bond 0.00254 (19847) covalent geometry : angle 0.49972 (26985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6888 (t70) REVERT: A 88 ASP cc_start: 0.7793 (m-30) cc_final: 0.7556 (m-30) REVERT: A 190 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6393 (mpt-90) REVERT: A 309 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7536 (mp0) REVERT: A 544 ASN cc_start: 0.7456 (m110) cc_final: 0.7115 (m-40) REVERT: A 820 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: A 856 ASN cc_start: 0.7734 (m110) cc_final: 0.7424 (m110) REVERT: A 1138 TYR cc_start: 0.7048 (m-80) cc_final: 0.6780 (m-80) REVERT: B 282 ASN cc_start: 0.6992 (m-40) cc_final: 0.5797 (t0) REVERT: B 558 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7418 (mmmm) REVERT: B 1010 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7694 (pt0) REVERT: C 50 SER cc_start: 0.8889 (t) cc_final: 0.8683 (m) REVERT: C 773 GLU cc_start: 0.8070 (tt0) cc_final: 0.7859 (tt0) REVERT: C 921 LYS cc_start: 0.8370 (ttpp) cc_final: 0.7884 (mttp) outliers start: 24 outliers final: 8 residues processed: 198 average time/residue: 1.1674 time to fit residues: 265.3518 Evaluate side-chains 173 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 9 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 969 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 564 GLN C 690 GLN C 957 GLN C1002 GLN C1083 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118390 restraints weight = 20628.871| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.98 r_work: 0.3228 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 19902 Z= 0.272 Angle : 0.661 14.880 27123 Z= 0.339 Chirality : 0.049 0.206 3225 Planarity : 0.005 0.057 3425 Dihedral : 6.699 59.567 3201 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.01 % Allowed : 9.69 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2383 helix: 2.31 (0.21), residues: 602 sheet: 0.81 (0.21), residues: 541 loop : -0.97 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 886 HIS 0.008 0.002 HIS C1083 PHE 0.038 0.002 PHE A 906 TYR 0.024 0.002 TYR A1067 ARG 0.005 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 27) link_NAG-ASN : angle 3.05920 ( 81) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.70578 ( 3) hydrogen bonds : bond 0.06036 ( 864) hydrogen bonds : angle 5.50881 ( 2418) SS BOND : bond 0.00805 ( 27) SS BOND : angle 1.99420 ( 54) covalent geometry : bond 0.00678 (19847) covalent geometry : angle 0.63493 (26985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 2.097 Fit side-chains REVERT: A 88 ASP cc_start: 0.7860 (m-30) cc_final: 0.7643 (m-30) REVERT: A 190 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6020 (mpt-90) REVERT: A 309 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 544 ASN cc_start: 0.7501 (m110) cc_final: 0.7094 (m-40) REVERT: A 820 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: A 856 ASN cc_start: 0.7899 (m110) cc_final: 0.7546 (m110) REVERT: A 957 GLN cc_start: 0.8175 (tp40) cc_final: 0.7967 (mm110) REVERT: A 969 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8099 (t0) REVERT: A 1138 TYR cc_start: 0.7129 (m-80) cc_final: 0.6762 (m-80) REVERT: B 287 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.6971 (t0) REVERT: B 558 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7382 (mmmm) REVERT: B 603 ASN cc_start: 0.7394 (t0) cc_final: 0.7141 (p0) REVERT: B 1010 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7609 (pt0) REVERT: C 309 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: C 902 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8395 (tpt) outliers start: 43 outliers final: 21 residues processed: 197 average time/residue: 1.1532 time to fit residues: 261.9629 Evaluate side-chains 176 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 57 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 182 optimal weight: 0.0770 chunk 243 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 901 GLN C 564 GLN C 690 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124388 restraints weight = 20652.721| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.97 r_work: 0.3248 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19902 Z= 0.116 Angle : 0.527 13.451 27123 Z= 0.271 Chirality : 0.044 0.185 3225 Planarity : 0.004 0.051 3425 Dihedral : 6.091 59.795 3201 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 1.73 % Allowed : 11.79 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2383 helix: 2.74 (0.21), residues: 599 sheet: 0.86 (0.21), residues: 544 loop : -0.90 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS B1088 PHE 0.018 0.001 PHE A 168 TYR 0.018 0.001 TYR C 369 ARG 0.002 0.000 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 27) link_NAG-ASN : angle 2.72861 ( 81) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.14960 ( 3) hydrogen bonds : bond 0.04368 ( 864) hydrogen bonds : angle 5.10943 ( 2418) SS BOND : bond 0.00411 ( 27) SS BOND : angle 1.27766 ( 54) covalent geometry : bond 0.00262 (19847) covalent geometry : angle 0.50351 (26985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7898 (m-30) cc_final: 0.7653 (m-30) REVERT: A 205 SER cc_start: 0.8654 (m) cc_final: 0.8424 (t) REVERT: A 309 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7272 (mp0) REVERT: A 544 ASN cc_start: 0.7100 (m110) cc_final: 0.6706 (m-40) REVERT: A 856 ASN cc_start: 0.7763 (m110) cc_final: 0.7438 (m110) REVERT: A 1138 TYR cc_start: 0.7071 (m-80) cc_final: 0.6689 (m-80) REVERT: B 558 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7348 (mmmm) REVERT: B 904 TYR cc_start: 0.8199 (m-10) cc_final: 0.7751 (m-10) REVERT: B 1010 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7688 (pt0) REVERT: C 902 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8244 (tpt) outliers start: 37 outliers final: 18 residues processed: 188 average time/residue: 1.1331 time to fit residues: 246.1919 Evaluate side-chains 172 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 76 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 177 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN A 957 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 901 GLN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121219 restraints weight = 20864.201| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.94 r_work: 0.3192 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19902 Z= 0.229 Angle : 0.621 14.343 27123 Z= 0.317 Chirality : 0.048 0.199 3225 Planarity : 0.004 0.045 3425 Dihedral : 6.201 59.014 3201 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.81 % Allowed : 12.07 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2383 helix: 2.55 (0.21), residues: 586 sheet: 0.65 (0.21), residues: 563 loop : -1.03 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.004 0.001 HIS A1088 PHE 0.016 0.002 PHE C1121 TYR 0.021 0.002 TYR C1067 ARG 0.003 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 27) link_NAG-ASN : angle 3.07025 ( 81) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 1.57737 ( 3) hydrogen bonds : bond 0.05578 ( 864) hydrogen bonds : angle 5.34098 ( 2418) SS BOND : bond 0.00709 ( 27) SS BOND : angle 1.63449 ( 54) covalent geometry : bond 0.00567 (19847) covalent geometry : angle 0.59467 (26985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8006 (m-30) cc_final: 0.7786 (m-30) REVERT: A 188 ASN cc_start: 0.6897 (p0) cc_final: 0.6195 (p0) REVERT: A 190 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6094 (mpt-90) REVERT: A 309 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7193 (mp0) REVERT: A 540 ASN cc_start: 0.7118 (t0) cc_final: 0.6881 (m-40) REVERT: A 544 ASN cc_start: 0.7140 (m110) cc_final: 0.6731 (m-40) REVERT: A 745 ASP cc_start: 0.7828 (t70) cc_final: 0.7543 (t70) REVERT: A 751 ASN cc_start: 0.8675 (m-40) cc_final: 0.8439 (m110) REVERT: A 856 ASN cc_start: 0.7947 (m110) cc_final: 0.7611 (m110) REVERT: A 1002 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: A 1138 TYR cc_start: 0.7142 (m-80) cc_final: 0.6729 (m-80) REVERT: B 287 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7030 (t0) REVERT: B 558 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7452 (mmmm) REVERT: B 603 ASN cc_start: 0.7539 (t0) cc_final: 0.7199 (p0) REVERT: B 675 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: B 904 TYR cc_start: 0.8232 (m-10) cc_final: 0.7815 (m-10) REVERT: B 916 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 1010 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7691 (pt0) REVERT: C 309 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: C 787 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: C 902 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8390 (tpt) outliers start: 60 outliers final: 32 residues processed: 198 average time/residue: 1.1051 time to fit residues: 253.4842 Evaluate side-chains 193 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 613 GLN A 957 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 901 GLN C 564 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123777 restraints weight = 20708.624| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.97 r_work: 0.3233 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19902 Z= 0.135 Angle : 0.541 14.067 27123 Z= 0.277 Chirality : 0.044 0.179 3225 Planarity : 0.004 0.044 3425 Dihedral : 5.983 59.789 3201 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.39 % Allowed : 13.06 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2383 helix: 2.74 (0.21), residues: 592 sheet: 0.73 (0.21), residues: 561 loop : -1.00 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.017 0.001 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 27) link_NAG-ASN : angle 2.82171 ( 81) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 1.20261 ( 3) hydrogen bonds : bond 0.04571 ( 864) hydrogen bonds : angle 5.11949 ( 2418) SS BOND : bond 0.00472 ( 27) SS BOND : angle 1.36003 ( 54) covalent geometry : bond 0.00321 (19847) covalent geometry : angle 0.51616 (26985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7998 (m-30) cc_final: 0.7790 (m-30) REVERT: A 190 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6126 (mpt-90) REVERT: A 309 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7211 (mp0) REVERT: A 540 ASN cc_start: 0.7015 (t0) cc_final: 0.6797 (m-40) REVERT: A 544 ASN cc_start: 0.6935 (m110) cc_final: 0.6542 (m-40) REVERT: A 751 ASN cc_start: 0.8683 (m-40) cc_final: 0.8458 (m110) REVERT: A 856 ASN cc_start: 0.7909 (m110) cc_final: 0.7578 (m110) REVERT: A 1002 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: A 1138 TYR cc_start: 0.7140 (m-80) cc_final: 0.6746 (m-80) REVERT: B 287 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7054 (t0) REVERT: B 558 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7439 (mmmm) REVERT: B 675 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: B 904 TYR cc_start: 0.8190 (m-10) cc_final: 0.7620 (m-10) REVERT: B 916 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8209 (tt) REVERT: B 1010 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7701 (pt0) REVERT: C 787 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: C 902 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8421 (tpt) outliers start: 51 outliers final: 28 residues processed: 194 average time/residue: 1.0689 time to fit residues: 240.3924 Evaluate side-chains 187 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 210 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 229 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 564 GLN C 804 GLN C 935 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122830 restraints weight = 20689.913| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.96 r_work: 0.3266 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19902 Z= 0.108 Angle : 0.517 13.531 27123 Z= 0.265 Chirality : 0.043 0.176 3225 Planarity : 0.003 0.041 3425 Dihedral : 5.777 59.677 3201 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 13.48 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2383 helix: 2.79 (0.21), residues: 605 sheet: 0.77 (0.21), residues: 577 loop : -0.95 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 PHE 0.019 0.001 PHE C 86 TYR 0.018 0.001 TYR C 369 ARG 0.001 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 27) link_NAG-ASN : angle 2.62043 ( 81) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 1.10399 ( 3) hydrogen bonds : bond 0.04069 ( 864) hydrogen bonds : angle 4.96007 ( 2418) SS BOND : bond 0.00426 ( 27) SS BOND : angle 1.50605 ( 54) covalent geometry : bond 0.00242 (19847) covalent geometry : angle 0.49378 (26985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7993 (m-30) cc_final: 0.7774 (m-30) REVERT: A 309 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7164 (mp0) REVERT: A 544 ASN cc_start: 0.6665 (m110) cc_final: 0.6268 (m-40) REVERT: A 856 ASN cc_start: 0.7698 (m110) cc_final: 0.7384 (m110) REVERT: A 1002 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 1138 TYR cc_start: 0.7108 (m-80) cc_final: 0.6729 (m-80) REVERT: B 287 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7014 (t0) REVERT: B 558 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7413 (mmmm) REVERT: B 580 GLN cc_start: 0.5439 (OUTLIER) cc_final: 0.5133 (mp10) REVERT: B 902 MET cc_start: 0.8653 (mmp) cc_final: 0.8408 (mmp) REVERT: B 904 TYR cc_start: 0.8145 (m-10) cc_final: 0.7519 (m-10) REVERT: B 916 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8185 (tt) REVERT: B 1010 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7660 (pt0) REVERT: B 1113 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: C 380 TYR cc_start: 0.7508 (m-80) cc_final: 0.7227 (m-10) REVERT: C 804 GLN cc_start: 0.8095 (mt0) cc_final: 0.7675 (mm110) REVERT: C 902 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8392 (tpt) outliers start: 42 outliers final: 27 residues processed: 196 average time/residue: 1.1564 time to fit residues: 261.4348 Evaluate side-chains 189 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 92 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN C 564 GLN C 804 GLN C 935 GLN C 957 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120024 restraints weight = 20819.796| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.94 r_work: 0.3244 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19902 Z= 0.173 Angle : 0.568 13.605 27123 Z= 0.291 Chirality : 0.045 0.179 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.926 59.684 3201 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 2.39 % Allowed : 13.62 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2383 helix: 2.69 (0.21), residues: 598 sheet: 0.73 (0.21), residues: 564 loop : -0.99 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.016 0.002 PHE C 86 TYR 0.033 0.002 TYR A 904 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 27) link_NAG-ASN : angle 2.78162 ( 81) link_BETA1-4 : bond 0.00448 ( 1) link_BETA1-4 : angle 1.39786 ( 3) hydrogen bonds : bond 0.04852 ( 864) hydrogen bonds : angle 5.09719 ( 2418) SS BOND : bond 0.00549 ( 27) SS BOND : angle 1.99006 ( 54) covalent geometry : bond 0.00424 (19847) covalent geometry : angle 0.54170 (26985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7995 (m-30) cc_final: 0.7773 (m-30) REVERT: A 309 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7074 (mp0) REVERT: A 544 ASN cc_start: 0.6695 (m110) cc_final: 0.6284 (m-40) REVERT: A 751 ASN cc_start: 0.8618 (m-40) cc_final: 0.8396 (m110) REVERT: A 856 ASN cc_start: 0.7843 (m110) cc_final: 0.7504 (m110) REVERT: A 1002 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: A 1138 TYR cc_start: 0.7109 (m-80) cc_final: 0.6698 (m-80) REVERT: B 287 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6959 (t0) REVERT: B 558 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7421 (mmmm) REVERT: B 702 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 904 TYR cc_start: 0.8196 (m-10) cc_final: 0.7524 (m-10) REVERT: B 916 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8172 (tt) REVERT: B 1010 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7597 (pt0) REVERT: C 226 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6546 (mp) REVERT: C 380 TYR cc_start: 0.7581 (m-80) cc_final: 0.7263 (m-10) REVERT: C 787 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 804 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7665 (mm110) REVERT: C 902 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8401 (tpt) outliers start: 51 outliers final: 32 residues processed: 197 average time/residue: 1.1098 time to fit residues: 253.4266 Evaluate side-chains 197 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 89 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 238 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN C 564 GLN C 804 GLN C 957 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122223 restraints weight = 20717.422| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.96 r_work: 0.3243 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19902 Z= 0.136 Angle : 0.540 13.275 27123 Z= 0.277 Chirality : 0.044 0.171 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.866 59.655 3201 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 1.87 % Allowed : 14.32 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2383 helix: 2.80 (0.21), residues: 592 sheet: 0.73 (0.21), residues: 567 loop : -0.96 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.017 0.001 PHE C 86 TYR 0.021 0.001 TYR A 904 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 27) link_NAG-ASN : angle 2.68872 ( 81) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 1.25251 ( 3) hydrogen bonds : bond 0.04480 ( 864) hydrogen bonds : angle 5.01840 ( 2418) SS BOND : bond 0.00479 ( 27) SS BOND : angle 1.68639 ( 54) covalent geometry : bond 0.00325 (19847) covalent geometry : angle 0.51559 (26985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8009 (m-30) cc_final: 0.7790 (m-30) REVERT: A 237 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6923 (mtm110) REVERT: A 309 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7147 (mp0) REVERT: A 544 ASN cc_start: 0.6572 (m110) cc_final: 0.6162 (m-40) REVERT: A 856 ASN cc_start: 0.7870 (m110) cc_final: 0.7543 (m110) REVERT: A 1002 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: A 1138 TYR cc_start: 0.7131 (m-80) cc_final: 0.6736 (m-80) REVERT: B 287 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7040 (t0) REVERT: B 558 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7439 (mmmm) REVERT: B 580 GLN cc_start: 0.5544 (OUTLIER) cc_final: 0.5254 (mp10) REVERT: B 702 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: B 904 TYR cc_start: 0.8238 (m-10) cc_final: 0.7605 (m-10) REVERT: B 916 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 1010 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7691 (pt0) REVERT: C 380 TYR cc_start: 0.7557 (m-80) cc_final: 0.7265 (m-10) REVERT: C 804 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7620 (mm110) REVERT: C 902 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8409 (tpt) outliers start: 40 outliers final: 30 residues processed: 185 average time/residue: 1.0889 time to fit residues: 233.6995 Evaluate side-chains 195 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 804 GLN C 957 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125154 restraints weight = 20728.622| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.05 r_work: 0.3242 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19902 Z= 0.139 Angle : 0.543 13.110 27123 Z= 0.279 Chirality : 0.044 0.173 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.847 59.584 3201 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 1.92 % Allowed : 14.41 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2383 helix: 2.78 (0.21), residues: 593 sheet: 0.74 (0.21), residues: 567 loop : -0.95 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.017 0.001 PHE C 86 TYR 0.021 0.001 TYR A 904 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 27) link_NAG-ASN : angle 2.66594 ( 81) link_BETA1-4 : bond 0.00409 ( 1) link_BETA1-4 : angle 1.28291 ( 3) hydrogen bonds : bond 0.04475 ( 864) hydrogen bonds : angle 5.01055 ( 2418) SS BOND : bond 0.00478 ( 27) SS BOND : angle 1.61894 ( 54) covalent geometry : bond 0.00334 (19847) covalent geometry : angle 0.51959 (26985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 2.087 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8015 (m-30) cc_final: 0.7808 (m-30) REVERT: A 237 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7088 (mtp-110) REVERT: A 309 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7089 (mp0) REVERT: A 544 ASN cc_start: 0.6521 (m110) cc_final: 0.6107 (m-40) REVERT: A 751 ASN cc_start: 0.8620 (m-40) cc_final: 0.8405 (m110) REVERT: A 856 ASN cc_start: 0.7839 (m110) cc_final: 0.7504 (m110) REVERT: A 1002 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: A 1138 TYR cc_start: 0.7111 (m-80) cc_final: 0.6710 (m-80) REVERT: B 287 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7002 (t0) REVERT: B 558 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7249 (mmmm) REVERT: B 702 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: B 902 MET cc_start: 0.8520 (mmp) cc_final: 0.8219 (mmp) REVERT: B 904 TYR cc_start: 0.8237 (m-10) cc_final: 0.7603 (m-10) REVERT: B 916 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 1010 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7621 (pt0) REVERT: C 380 TYR cc_start: 0.7536 (m-80) cc_final: 0.7243 (m-10) REVERT: C 787 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: C 804 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7618 (mm110) REVERT: C 902 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8388 (tpt) outliers start: 41 outliers final: 32 residues processed: 187 average time/residue: 1.0831 time to fit residues: 235.2288 Evaluate side-chains 195 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 100 optimal weight: 0.0870 chunk 102 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 804 GLN C 957 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122763 restraints weight = 20876.345| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.95 r_work: 0.3264 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19902 Z= 0.111 Angle : 0.519 12.756 27123 Z= 0.267 Chirality : 0.043 0.183 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.714 59.003 3201 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.01 % Allowed : 14.23 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2383 helix: 2.87 (0.21), residues: 594 sheet: 0.80 (0.21), residues: 557 loop : -0.91 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 PHE 0.018 0.001 PHE C 86 TYR 0.018 0.001 TYR A 904 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 27) link_NAG-ASN : angle 2.53300 ( 81) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 1.17066 ( 3) hydrogen bonds : bond 0.04071 ( 864) hydrogen bonds : angle 4.90198 ( 2418) SS BOND : bond 0.00408 ( 27) SS BOND : angle 1.45161 ( 54) covalent geometry : bond 0.00253 (19847) covalent geometry : angle 0.49752 (26985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15814.29 seconds wall clock time: 269 minutes 43.50 seconds (16183.50 seconds total)