Starting phenix.real_space_refine on Sun Aug 24 11:42:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyo_41727/08_2025/8tyo_41727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyo_41727/08_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_41727/08_2025/8tyo_41727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyo_41727/08_2025/8tyo_41727.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyo_41727/08_2025/8tyo_41727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyo_41727/08_2025/8tyo_41727.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.58, per 1000 atoms: 0.18 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: 1.43 Conformation dependent library (CDL) restraints added in 624.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.50 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: 3.46 Time building geometry restraints manager: 1.83 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 1309)) selection = (chain 'B' and (resid 27 through 130 or resid 168 through 676 or resid 690 throu \ gh 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 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: 1.050 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- 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 : 4.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (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 ARG 0.003 0.000 ARG C 319 TYR 0.017 0.001 TYR C 369 PHE 0.034 0.001 PHE A 906 TRP 0.026 0.002 TRP C 886 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00343 (19847) covalent geometry : angle 0.51472 (26985) SS BOND : bond 0.00384 ( 27) SS BOND : angle 1.37527 ( 54) hydrogen bonds : bond 0.14121 ( 864) hydrogen bonds : angle 6.55190 ( 2418) link_BETA1-4 : bond 0.00313 ( 1) link_BETA1-4 : angle 0.90441 ( 3) link_NAG-ASN : bond 0.00204 ( 27) link_NAG-ASN : angle 1.47854 ( 81) *********************** 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 : 0.695 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: 0.5124 time to fit residues: 132.5648 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 955 ASN A1101 HIS B 914 ASN C 87 ASN C 564 GLN C 804 GLN C 856 ASN C1002 GLN C1010 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.179412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120043 restraints weight = 20807.372| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.99 r_work: 0.3209 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19902 Z= 0.263 Angle : 0.647 8.145 27123 Z= 0.337 Chirality : 0.050 0.215 3225 Planarity : 0.005 0.072 3425 Dihedral : 7.661 74.753 3201 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 8.47 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2383 helix: 2.26 (0.21), residues: 602 sheet: 0.84 (0.21), residues: 549 loop : -0.98 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1014 TYR 0.026 0.002 TYR C 904 PHE 0.044 0.002 PHE A 906 TRP 0.029 0.003 TRP C 886 HIS 0.008 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00653 (19847) covalent geometry : angle 0.63145 (26985) SS BOND : bond 0.00750 ( 27) SS BOND : angle 1.77903 ( 54) hydrogen bonds : bond 0.05992 ( 864) hydrogen bonds : angle 5.57578 ( 2418) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 1.76257 ( 3) link_NAG-ASN : bond 0.00277 ( 27) link_NAG-ASN : angle 2.25377 ( 81) *********************** 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 211 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7913 (m-30) cc_final: 0.7673 (m-30) REVERT: A 190 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6335 (mpt-90) REVERT: A 309 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7385 (mp0) REVERT: A 544 ASN cc_start: 0.7484 (m110) cc_final: 0.7095 (m-40) REVERT: A 745 ASP cc_start: 0.7704 (t70) cc_final: 0.7454 (t70) REVERT: A 820 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 856 ASN cc_start: 0.7927 (m110) cc_final: 0.7583 (m110) REVERT: A 969 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 1138 TYR cc_start: 0.7102 (m-80) cc_final: 0.6759 (m-80) REVERT: B 558 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7360 (mmmm) REVERT: B 603 ASN cc_start: 0.7486 (t0) cc_final: 0.7194 (p0) REVERT: B 762 GLN cc_start: 0.8097 (tt0) cc_final: 0.7313 (mm110) REVERT: B 1010 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7659 (pt0) REVERT: C 723 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 902 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8308 (tpt) REVERT: C 1101 HIS cc_start: 0.7428 (m90) cc_final: 0.7186 (m90) outliers start: 38 outliers final: 17 residues processed: 198 average time/residue: 0.5030 time to fit residues: 114.1911 Evaluate side-chains 177 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1114 ILE 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 B residue 1136 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 901 GLN A 957 GLN A1101 HIS C 564 GLN C 690 GLN C 901 GLN C 957 GLN C1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121618 restraints weight = 20806.441| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.07 r_work: 0.3231 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19902 Z= 0.176 Angle : 0.582 14.362 27123 Z= 0.299 Chirality : 0.046 0.184 3225 Planarity : 0.004 0.057 3425 Dihedral : 6.740 59.752 3201 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 2.15 % Allowed : 10.72 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2383 helix: 2.44 (0.21), residues: 601 sheet: 0.77 (0.21), residues: 551 loop : -1.00 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1014 TYR 0.024 0.001 TYR C 904 PHE 0.020 0.002 PHE A 906 TRP 0.017 0.002 TRP C 886 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00428 (19847) covalent geometry : angle 0.55613 (26985) SS BOND : bond 0.00535 ( 27) SS BOND : angle 1.73269 ( 54) hydrogen bonds : bond 0.05144 ( 864) hydrogen bonds : angle 5.36401 ( 2418) link_BETA1-4 : bond 0.00570 ( 1) link_BETA1-4 : angle 1.29634 ( 3) link_NAG-ASN : bond 0.00596 ( 27) link_NAG-ASN : angle 2.85362 ( 81) *********************** 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 211 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.573 Fit side-chains REVERT: A 88 ASP cc_start: 0.7874 (m-30) cc_final: 0.7631 (m-30) REVERT: A 190 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6068 (mpt-90) REVERT: A 309 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7303 (mp0) REVERT: A 544 ASN cc_start: 0.7359 (m110) cc_final: 0.6958 (m-40) REVERT: A 820 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: A 856 ASN cc_start: 0.7913 (m110) cc_final: 0.7572 (m110) REVERT: A 969 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8161 (t0) REVERT: A 1002 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: A 1138 TYR cc_start: 0.7096 (m-80) cc_final: 0.6736 (m-80) REVERT: B 287 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7038 (t0) REVERT: B 558 LYS cc_start: 0.7639 (mmmt) cc_final: 0.7366 (mmmm) REVERT: B 904 TYR cc_start: 0.8165 (m-10) cc_final: 0.7759 (m-10) REVERT: B 1010 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7691 (pt0) REVERT: B 1113 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: C 790 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8157 (pttt) REVERT: C 1081 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8023 (mt) REVERT: C 1101 HIS cc_start: 0.7422 (m90) cc_final: 0.7151 (m90) outliers start: 46 outliers final: 22 residues processed: 195 average time/residue: 0.4708 time to fit residues: 105.7858 Evaluate side-chains 175 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 1002 GLN Chi-restraints excluded: chain A residue 1081 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 B residue 1113 GLN 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 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1081 ILE 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 99 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 192 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 157 optimal weight: 0.0000 chunk 9 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- 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 C 564 GLN C 690 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123351 restraints weight = 20727.717| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.93 r_work: 0.3222 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19902 Z= 0.169 Angle : 0.571 14.137 27123 Z= 0.294 Chirality : 0.045 0.181 3225 Planarity : 0.004 0.048 3425 Dihedral : 6.196 59.347 3201 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 3.09 % Allowed : 11.51 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2383 helix: 2.53 (0.21), residues: 599 sheet: 0.71 (0.21), residues: 553 loop : -0.99 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1014 TYR 0.027 0.001 TYR C 904 PHE 0.017 0.002 PHE A 168 TRP 0.015 0.002 TRP C 886 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00410 (19847) covalent geometry : angle 0.54408 (26985) SS BOND : bond 0.00568 ( 27) SS BOND : angle 1.68165 ( 54) hydrogen bonds : bond 0.04997 ( 864) hydrogen bonds : angle 5.24940 ( 2418) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 1.33882 ( 3) link_NAG-ASN : bond 0.00496 ( 27) link_NAG-ASN : angle 2.92535 ( 81) *********************** 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 223 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 0.565 Fit side-chains REVERT: A 88 ASP cc_start: 0.7964 (m-30) cc_final: 0.7734 (m-30) REVERT: A 190 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6130 (mpt-90) REVERT: A 205 SER cc_start: 0.8645 (m) cc_final: 0.8427 (t) REVERT: A 309 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7196 (mp0) REVERT: A 544 ASN cc_start: 0.7107 (m110) cc_final: 0.6712 (m-40) REVERT: A 820 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: A 856 ASN cc_start: 0.7903 (m110) cc_final: 0.7560 (m110) REVERT: A 969 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 1002 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 1138 TYR cc_start: 0.7126 (m-80) cc_final: 0.6734 (m-80) REVERT: B 287 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7023 (t0) REVERT: B 558 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7423 (mmmm) REVERT: B 675 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: B 904 TYR cc_start: 0.8239 (m-10) cc_final: 0.7639 (m-10) REVERT: B 916 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8169 (tt) REVERT: B 1010 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7661 (pt0) REVERT: B 1113 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: C 309 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: C 787 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: C 790 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (pttt) REVERT: C 804 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7687 (mm110) REVERT: C 902 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8383 (tpt) REVERT: C 1081 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8035 (mt) REVERT: C 1101 HIS cc_start: 0.7445 (m90) cc_final: 0.7158 (m90) outliers start: 66 outliers final: 28 residues processed: 206 average time/residue: 0.4970 time to fit residues: 118.1132 Evaluate side-chains 191 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 A residue 1002 GLN Chi-restraints excluded: chain A residue 1081 ILE 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 B residue 1113 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 991 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 0.0060 chunk 64 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 784 GLN A1101 HIS A1135 ASN B 901 GLN C 564 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124951 restraints weight = 20677.053| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.12 r_work: 0.3225 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19902 Z= 0.138 Angle : 0.540 14.011 27123 Z= 0.278 Chirality : 0.044 0.164 3225 Planarity : 0.004 0.044 3425 Dihedral : 5.977 59.899 3201 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 2.90 % Allowed : 12.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2383 helix: 2.68 (0.21), residues: 599 sheet: 0.75 (0.21), residues: 566 loop : -0.97 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1039 TYR 0.026 0.001 TYR C 904 PHE 0.018 0.001 PHE C 86 TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00327 (19847) covalent geometry : angle 0.51534 (26985) SS BOND : bond 0.00492 ( 27) SS BOND : angle 1.43112 ( 54) hydrogen bonds : bond 0.04564 ( 864) hydrogen bonds : angle 5.11565 ( 2418) link_BETA1-4 : bond 0.00469 ( 1) link_BETA1-4 : angle 1.19355 ( 3) link_NAG-ASN : bond 0.00432 ( 27) link_NAG-ASN : angle 2.77910 ( 81) *********************** 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 222 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 0.717 Fit side-chains REVERT: A 88 ASP cc_start: 0.8007 (m-30) cc_final: 0.7788 (m-30) REVERT: A 309 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7168 (mp0) REVERT: A 544 ASN cc_start: 0.6872 (m110) cc_final: 0.6477 (m-40) REVERT: A 820 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: A 856 ASN cc_start: 0.7775 (m110) cc_final: 0.7427 (m110) REVERT: A 969 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8095 (t0) REVERT: A 1002 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: A 1138 TYR cc_start: 0.7079 (m-80) cc_final: 0.6683 (m-80) REVERT: B 287 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.6995 (t0) REVERT: B 558 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7421 (mmmm) REVERT: B 904 TYR cc_start: 0.8253 (m-10) cc_final: 0.7604 (m-10) REVERT: B 916 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 1010 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7646 (pt0) REVERT: C 380 TYR cc_start: 0.7587 (m-80) cc_final: 0.7345 (m-10) REVERT: C 790 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8093 (pttt) REVERT: C 804 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: C 1081 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8057 (mt) REVERT: C 1101 HIS cc_start: 0.7470 (m90) cc_final: 0.7144 (m90) outliers start: 62 outliers final: 29 residues processed: 200 average time/residue: 0.4479 time to fit residues: 103.9380 Evaluate side-chains 193 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 701 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 A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1081 ILE 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 705 VAL Chi-restraints excluded: chain B residue 723 THR 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 B residue 1127 ASP 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 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL 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 233 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A1101 HIS B 675 GLN C 564 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123302 restraints weight = 20636.722| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.05 r_work: 0.3236 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19902 Z= 0.120 Angle : 0.519 13.691 27123 Z= 0.268 Chirality : 0.044 0.165 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.809 59.973 3201 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 12.82 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.17), residues: 2383 helix: 2.88 (0.21), residues: 588 sheet: 0.75 (0.21), residues: 572 loop : -0.89 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1091 TYR 0.022 0.001 TYR A 904 PHE 0.018 0.001 PHE C 86 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00280 (19847) covalent geometry : angle 0.49690 (26985) SS BOND : bond 0.00436 ( 27) SS BOND : angle 1.21959 ( 54) hydrogen bonds : bond 0.04274 ( 864) hydrogen bonds : angle 5.00293 ( 2418) link_BETA1-4 : bond 0.00325 ( 1) link_BETA1-4 : angle 1.16966 ( 3) link_NAG-ASN : bond 0.00399 ( 27) link_NAG-ASN : angle 2.65533 ( 81) *********************** 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 232 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 0.557 Fit side-chains REVERT: A 88 ASP cc_start: 0.8006 (m-30) cc_final: 0.7783 (m-30) REVERT: A 309 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7164 (mp0) REVERT: A 544 ASN cc_start: 0.6695 (m110) cc_final: 0.6294 (m-40) REVERT: A 751 ASN cc_start: 0.8638 (m-40) cc_final: 0.8418 (m110) REVERT: A 820 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: A 856 ASN cc_start: 0.7744 (m110) cc_final: 0.7400 (m110) REVERT: A 969 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 1002 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: A 1138 TYR cc_start: 0.7095 (m-80) cc_final: 0.6665 (m-80) REVERT: B 287 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7050 (t0) REVERT: B 558 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7432 (mmmm) REVERT: B 580 GLN cc_start: 0.5534 (OUTLIER) cc_final: 0.5219 (mp10) REVERT: B 675 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: B 702 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 916 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8189 (tt) REVERT: B 1010 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7663 (pt0) REVERT: C 380 TYR cc_start: 0.7476 (m-80) cc_final: 0.7218 (m-10) REVERT: C 787 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: C 804 GLN cc_start: 0.8223 (mt0) cc_final: 0.7725 (mm110) REVERT: C 1081 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8106 (mt) REVERT: C 1101 HIS cc_start: 0.7487 (m90) cc_final: 0.7131 (m90) outliers start: 62 outliers final: 30 residues processed: 210 average time/residue: 0.4592 time to fit residues: 111.9150 Evaluate side-chains 198 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 580 GLN 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 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 883 THR 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 701 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A1101 HIS B 675 GLN C 564 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124216 restraints weight = 20687.187| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.99 r_work: 0.3234 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19902 Z= 0.134 Angle : 0.534 13.558 27123 Z= 0.275 Chirality : 0.044 0.162 3225 Planarity : 0.004 0.041 3425 Dihedral : 5.819 59.622 3201 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.95 % Allowed : 13.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2383 helix: 2.86 (0.21), residues: 588 sheet: 0.74 (0.21), residues: 569 loop : -0.90 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1039 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE C 86 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00318 (19847) covalent geometry : angle 0.50880 (26985) SS BOND : bond 0.00456 ( 27) SS BOND : angle 1.80043 ( 54) hydrogen bonds : bond 0.04395 ( 864) hydrogen bonds : angle 5.01501 ( 2418) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 1.25240 ( 3) link_NAG-ASN : bond 0.00389 ( 27) link_NAG-ASN : angle 2.64594 ( 81) *********************** 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 225 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8005 (m-30) cc_final: 0.7799 (m-30) REVERT: A 309 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7166 (mp0) REVERT: A 312 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 544 ASN cc_start: 0.6538 (m110) cc_final: 0.6129 (m-40) REVERT: A 820 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: A 856 ASN cc_start: 0.7745 (m110) cc_final: 0.7415 (m110) REVERT: A 969 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8183 (t0) REVERT: A 1002 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: A 1138 TYR cc_start: 0.7100 (m-80) cc_final: 0.6661 (m-80) REVERT: B 287 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7062 (t0) REVERT: B 558 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7280 (mmmm) REVERT: B 580 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.5171 (mp10) REVERT: B 675 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: B 902 MET cc_start: 0.8755 (mmp) cc_final: 0.8459 (mmp) REVERT: B 916 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8191 (tt) REVERT: B 1010 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7688 (pt0) REVERT: C 226 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6692 (mp) REVERT: C 380 TYR cc_start: 0.7482 (m-80) cc_final: 0.7212 (m-10) REVERT: C 787 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: C 804 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7731 (mm110) REVERT: C 1081 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 1101 HIS cc_start: 0.7506 (m90) cc_final: 0.7182 (m90) outliers start: 63 outliers final: 37 residues processed: 205 average time/residue: 0.4846 time to fit residues: 115.5053 Evaluate side-chains 205 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 ILE 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 701 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 A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR 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 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 934 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS 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 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1081 ILE 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 75 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 219 optimal weight: 0.0040 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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 B 901 GLN C 564 GLN C 690 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120033 restraints weight = 20752.335| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.98 r_work: 0.3195 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19902 Z= 0.253 Angle : 0.636 13.966 27123 Z= 0.328 Chirality : 0.048 0.206 3225 Planarity : 0.004 0.041 3425 Dihedral : 6.171 59.289 3201 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 3.28 % Allowed : 13.20 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2383 helix: 2.47 (0.21), residues: 583 sheet: 0.61 (0.21), residues: 553 loop : -1.08 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1014 TYR 0.022 0.002 TYR A1067 PHE 0.015 0.002 PHE A1121 TRP 0.016 0.002 TRP C 886 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00629 (19847) covalent geometry : angle 0.61127 (26985) SS BOND : bond 0.00874 ( 27) SS BOND : angle 1.70115 ( 54) hydrogen bonds : bond 0.05734 ( 864) hydrogen bonds : angle 5.34849 ( 2418) link_BETA1-4 : bond 0.00539 ( 1) link_BETA1-4 : angle 1.72330 ( 3) link_NAG-ASN : bond 0.00447 ( 27) link_NAG-ASN : angle 3.00344 ( 81) *********************** 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 231 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7090 (mp0) REVERT: A 544 ASN cc_start: 0.6593 (m110) cc_final: 0.6169 (m-40) REVERT: A 565 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: A 745 ASP cc_start: 0.7916 (t70) cc_final: 0.7588 (t70) REVERT: A 751 ASN cc_start: 0.8652 (m-40) cc_final: 0.8421 (m110) REVERT: A 820 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 856 ASN cc_start: 0.7907 (m110) cc_final: 0.7562 (m110) REVERT: A 969 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 1002 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: A 1138 TYR cc_start: 0.7190 (m-80) cc_final: 0.6759 (m-80) REVERT: B 287 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 558 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7255 (mmmm) REVERT: B 603 ASN cc_start: 0.7554 (t0) cc_final: 0.7185 (p0) REVERT: B 702 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 916 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 1010 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7674 (pt0) REVERT: B 1113 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: C 309 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: C 380 TYR cc_start: 0.7745 (m-80) cc_final: 0.7405 (m-10) REVERT: C 787 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: C 804 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7713 (mm110) REVERT: C 1081 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8039 (mt) REVERT: C 1101 HIS cc_start: 0.7449 (m90) cc_final: 0.7088 (m90) outliers start: 70 outliers final: 46 residues processed: 212 average time/residue: 0.4667 time to fit residues: 115.2782 Evaluate side-chains 213 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 565 PHE 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 701 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU 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 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU 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 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE 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 145 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123509 restraints weight = 20584.923| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.13 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19902 Z= 0.118 Angle : 0.525 13.220 27123 Z= 0.272 Chirality : 0.044 0.233 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.867 59.567 3201 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 2.57 % Allowed : 14.32 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2383 helix: 2.84 (0.21), residues: 588 sheet: 0.70 (0.21), residues: 557 loop : -0.97 (0.16), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR C 904 PHE 0.019 0.001 PHE C 86 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00271 (19847) covalent geometry : angle 0.50312 (26985) SS BOND : bond 0.00521 ( 27) SS BOND : angle 1.16674 ( 54) hydrogen bonds : bond 0.04225 ( 864) hydrogen bonds : angle 5.00042 ( 2418) link_BETA1-4 : bond 0.00484 ( 1) link_BETA1-4 : angle 1.12733 ( 3) link_NAG-ASN : bond 0.00556 ( 27) link_NAG-ASN : angle 2.66627 ( 81) *********************** 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 231 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7102 (mp0) REVERT: A 544 ASN cc_start: 0.6510 (m110) cc_final: 0.6113 (m-40) REVERT: A 820 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: A 856 ASN cc_start: 0.7825 (m110) cc_final: 0.7487 (m110) REVERT: A 969 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 1002 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: A 1138 TYR cc_start: 0.7110 (m-80) cc_final: 0.6694 (m-80) REVERT: B 287 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7011 (t0) REVERT: B 558 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7226 (mmmm) REVERT: B 916 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 1010 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7632 (pt0) REVERT: B 1113 GLN cc_start: 0.8428 (mp10) cc_final: 0.8201 (mp10) REVERT: C 380 TYR cc_start: 0.7579 (m-80) cc_final: 0.7281 (m-10) REVERT: C 563 GLN cc_start: 0.8053 (mt0) cc_final: 0.7629 (mt0) REVERT: C 804 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7723 (mm110) REVERT: C 935 GLN cc_start: 0.7178 (mt0) cc_final: 0.6779 (mt0) REVERT: C 1081 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8070 (mt) REVERT: C 1101 HIS cc_start: 0.7475 (m90) cc_final: 0.7178 (m90) outliers start: 55 outliers final: 37 residues processed: 214 average time/residue: 0.4866 time to fit residues: 121.4609 Evaluate side-chains 207 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 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 A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 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 705 VAL Chi-restraints excluded: chain B residue 723 THR 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 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 301 CYS 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 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE 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 14 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 154 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 955 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123186 restraints weight = 20719.970| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.00 r_work: 0.3243 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19902 Z= 0.125 Angle : 0.529 12.888 27123 Z= 0.274 Chirality : 0.044 0.206 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.772 59.903 3201 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.29 % Allowed : 14.74 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2383 helix: 2.81 (0.21), residues: 594 sheet: 0.74 (0.21), residues: 557 loop : -0.95 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE C 86 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00293 (19847) covalent geometry : angle 0.50754 (26985) SS BOND : bond 0.00543 ( 27) SS BOND : angle 1.21156 ( 54) hydrogen bonds : bond 0.04301 ( 864) hydrogen bonds : angle 4.97880 ( 2418) link_BETA1-4 : bond 0.00399 ( 1) link_BETA1-4 : angle 1.27653 ( 3) link_NAG-ASN : bond 0.00394 ( 27) link_NAG-ASN : angle 2.64176 ( 81) ********************** 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 221 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7205 (mtp-110) REVERT: A 309 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7081 (mp0) REVERT: A 544 ASN cc_start: 0.6517 (m110) cc_final: 0.6111 (m-40) REVERT: A 745 ASP cc_start: 0.7738 (t70) cc_final: 0.7464 (t70) REVERT: A 820 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: A 856 ASN cc_start: 0.7814 (m110) cc_final: 0.7478 (m110) REVERT: A 969 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8064 (t0) REVERT: A 1002 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: A 1138 TYR cc_start: 0.7112 (m-80) cc_final: 0.6711 (m-80) REVERT: B 287 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7009 (t0) REVERT: B 558 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7238 (mmmm) REVERT: B 902 MET cc_start: 0.8475 (mmp) cc_final: 0.8145 (mmp) REVERT: B 916 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 1010 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7613 (pt0) REVERT: C 380 TYR cc_start: 0.7538 (m-80) cc_final: 0.7248 (m-10) REVERT: C 563 GLN cc_start: 0.8096 (mt0) cc_final: 0.7655 (mt0) REVERT: C 804 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: C 1081 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8060 (mt) REVERT: C 1101 HIS cc_start: 0.7466 (m90) cc_final: 0.7165 (m90) outliers start: 49 outliers final: 40 residues processed: 205 average time/residue: 0.4499 time to fit residues: 107.5336 Evaluate side-chains 212 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 547 THR 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 701 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 916 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 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 705 VAL Chi-restraints excluded: chain B residue 723 THR 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 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 301 CYS 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 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE 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 206 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A1101 HIS A1125 ASN C 564 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126138 restraints weight = 20713.934| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.97 r_work: 0.3248 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19902 Z= 0.112 Angle : 0.515 12.357 27123 Z= 0.267 Chirality : 0.043 0.229 3225 Planarity : 0.004 0.043 3425 Dihedral : 5.648 59.274 3201 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.11 % Allowed : 14.93 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2383 helix: 2.91 (0.21), residues: 593 sheet: 0.75 (0.21), residues: 558 loop : -0.87 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.017 0.001 TYR C1067 PHE 0.018 0.001 PHE C 86 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00256 (19847) covalent geometry : angle 0.49536 (26985) SS BOND : bond 0.00486 ( 27) SS BOND : angle 1.08045 ( 54) hydrogen bonds : bond 0.04006 ( 864) hydrogen bonds : angle 4.86371 ( 2418) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 1.13199 ( 3) link_NAG-ASN : bond 0.00395 ( 27) link_NAG-ASN : angle 2.51357 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7037.72 seconds wall clock time: 120 minutes 17.27 seconds (7217.27 seconds total)