Starting phenix.real_space_refine on Thu Mar 5 16:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwn_23551/03_2026/7lwn_23551.map" } resolution = 2.94 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= 0.087 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 101 5.16 5 C 15046 2.51 5 N 3879 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23570 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7682 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7699 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7671 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.24, per 1000 atoms: 0.26 Number of scatterers: 23570 At special positions: 0 Unit cell: (129.349, 136.832, 193.489, 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 101 16.00 O 4544 8.00 N 3879 7.00 C 15046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.93 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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 480 " - pdb=" SG CYS C 488 " 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 165 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C 717 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1134 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN C1098 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 45 sheets defined 27.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.577A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.599A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.735A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.764A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.603A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.146A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.883A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.671A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.719A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.631A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.687A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.682A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.823A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.811A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.263A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.678A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 984 removed outlier: 3.525A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.017A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.505A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.964A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.508A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.531A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.588A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.944A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.562A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.578A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.675A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.625A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.683A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.675A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.358A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.196A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.994A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.252A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.324A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.603A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.416A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.512A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.822A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.130A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.506A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.303A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.393A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.595A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.004A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.481A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.732A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.779A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.987A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.977A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.826A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.504A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.242A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.401A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.597A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2841 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: 5.01 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6174 1.33 - 1.46: 4519 1.46 - 1.58: 13260 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24078 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.79e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.41e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.40e+01 bond pdb=" C5 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 24073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 25337 2.12 - 4.24: 6869 4.24 - 6.36: 527 6.36 - 8.49: 30 8.49 - 10.61: 3 Bond angle restraints: 32766 Sorted by residual: angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.44e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.08e+01 angle pdb=" CA PHE B 643 " pdb=" CB PHE B 643 " pdb=" CG PHE B 643 " ideal model delta sigma weight residual 113.80 119.33 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" OE1 GLN C1113 " pdb=" CD GLN C1113 " pdb=" NE2 GLN C1113 " ideal model delta sigma weight residual 122.60 117.18 5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.20 -5.40 1.00e+00 1.00e+00 2.92e+01 ... (remaining 32761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 13790 17.46 - 34.91: 763 34.91 - 52.37: 139 52.37 - 69.83: 65 69.83 - 87.28: 24 Dihedral angle restraints: 14781 sinusoidal: 6127 harmonic: 8654 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 177.21 -84.21 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.69 67.69 1 1.00e+01 1.00e-02 5.96e+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 93.00 147.37 -54.37 1 1.00e+01 1.00e-02 4.01e+01 ... (remaining 14778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2296 0.079 - 0.157: 1264 0.157 - 0.236: 255 0.236 - 0.314: 53 0.314 - 0.393: 10 Chirality restraints: 3878 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.70e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.76e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.07e+01 ... (remaining 3875 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.351 2.00e-02 2.50e+03 1.93e-01 9.31e+02 pdb=" CG TRP C 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.180 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.146 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.286 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.213 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.073 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 269 " -0.175 2.00e-02 2.50e+03 9.13e-02 1.67e+02 pdb=" CG TYR A 269 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 269 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR A 269 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 269 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 269 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 269 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 269 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " -0.106 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" CG ASN A1134 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " 0.176 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.136 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11291 2.99 - 3.47: 22038 3.47 - 3.95: 39068 3.95 - 4.42: 43381 4.42 - 4.90: 73416 Nonbonded interactions: 189194 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.516 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.517 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.519 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.529 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.537 3.040 ... (remaining 189189 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 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 o \ r (resid 867 through 868 and (name N or name CA or name C or name O or name CB ) \ ) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and ( \ name N or name CA or name C or name O or name CB )) or resid 1147 through 1307)) \ selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 130 or (resid 131 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 164 or (resid 166 and (name N or name CA or name C or name O or nam \ e CB )) or resid 167 through 168 or (resid 169 and (name N or name CA or name C \ or name O or name CB )) or resid 170 through 190 or (resid 191 and (name N or na \ me CA or name C or name O or name CB )) or resid 192 through 195 or (resid 196 t \ hrough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 241 or (resid 242 through 264 and (name N or name CA or name C or name \ O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name CA or \ name C or name O or name CB )) or resid 282 through 479 or (resid 480 and (name \ N or name CA or name C or name O or name CB )) or resid 481 through 483 or resi \ d 485 through 567 or (resid 568 and (name N or name CA or name C or name O or na \ me CB )) or resid 569 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 through 618 or (resid 619 \ and (name N or name CA or name C or name O or name CB )) or resid 620 through 67 \ 6 or resid 690 through 744 or (resid 745 and (name N or name CA or name C or nam \ e O or name CB )) or resid 746 through 747 or (resid 748 and (name N or name CA \ or name C or name O or name CB )) or resid 749 through 810 or (resid 811 and (na \ me N or name CA or name C or name O or name CB )) or resid 813 or (resid 814 and \ (name N or name CA or name C or name O or name CB )) or resid 815 through 827 o \ r resid 855 through 866 or (resid 867 through 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 1091 or (resid 1092 and (name N \ or name CA or name C or name O or name CB )) or resid 1093 through 1143 or (resi \ d 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or \ resid 1147 through 1307)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 130 or (resid 131 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 143 or ( \ resid 165 through 166 and (name N or name CA or name C or name O or name CB )) o \ r resid 167 through 195 or (resid 196 through 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 213 or (resid 214 through 215 an \ d (name N or name CA or name C or name O or name CB )) or resid 216 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 308 or (resid 309 and (name N or name CA or name C o \ r name O or name CB )) or resid 310 through 479 or (resid 480 and (name N or nam \ e CA or name C or name O or name CB )) or resid 481 through 483 or resid 485 thr \ ough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 567 or (resid 568 and (name N or name CA or name C or name \ O or name CB )) or resid 569 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 618 or (res \ id 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thr \ ough 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) \ or resid 815 through 1091 or (resid 1092 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1093 through 1141 or (resid 1142 and (name N or name \ CA or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 through 13 \ 07)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.010 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.170 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.013 0.099 24152 Z= 0.772 Angle : 1.786 10.606 32951 Z= 1.192 Chirality : 0.094 0.393 3878 Planarity : 0.013 0.228 4177 Dihedral : 12.608 87.283 9094 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.58 % Favored : 95.14 % Rotamer: Outliers : 0.87 % Allowed : 2.24 % Favored : 96.89 % Cbeta Deviations : 0.14 % 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 are not related in a simple way. whole: -0.76 (0.14), residues: 2924 helix: -1.06 (0.16), residues: 682 sheet: 0.89 (0.20), residues: 578 loop : -0.74 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.175 0.021 TYR A 269 PHE 0.087 0.012 PHE B 718 TRP 0.351 0.031 TRP C 886 HIS 0.015 0.003 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01338 (24078) covalent geometry : angle 1.76915 (32766) SS BOND : bond 0.02051 ( 37) SS BOND : angle 2.29990 ( 74) hydrogen bonds : bond 0.15502 ( 1029) hydrogen bonds : angle 8.16479 ( 2841) link_BETA1-4 : bond 0.02408 ( 5) link_BETA1-4 : angle 3.93730 ( 15) link_NAG-ASN : bond 0.01349 ( 32) link_NAG-ASN : angle 4.49925 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 371 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7156 (m-90) cc_final: 0.6916 (m-90) REVERT: A 205 SER cc_start: 0.8680 (p) cc_final: 0.8359 (t) REVERT: A 529 LYS cc_start: 0.8045 (mttt) cc_final: 0.7277 (mppt) REVERT: A 565 PHE cc_start: 0.7694 (p90) cc_final: 0.7386 (p90) REVERT: B 329 PHE cc_start: 0.8450 (m-80) cc_final: 0.8230 (m-80) REVERT: B 697 MET cc_start: 0.8975 (ptm) cc_final: 0.8698 (ptp) REVERT: B 859 THR cc_start: 0.8873 (p) cc_final: 0.8646 (t) REVERT: B 935 GLN cc_start: 0.7979 (tt0) cc_final: 0.7659 (tt0) REVERT: B 1038 LYS cc_start: 0.8404 (tttm) cc_final: 0.8117 (ttmm) REVERT: C 106 PHE cc_start: 0.6966 (m-80) cc_final: 0.6464 (m-80) REVERT: C 117 LEU cc_start: 0.7231 (mp) cc_final: 0.6879 (tm) REVERT: C 129 LYS cc_start: 0.7791 (mttt) cc_final: 0.7086 (mttm) REVERT: C 237 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7428 (mtp85) REVERT: C 394 ASN cc_start: 0.7310 (m-40) cc_final: 0.7096 (m110) REVERT: C 453 PHE cc_start: 0.6826 (p90) cc_final: 0.6495 (p90) REVERT: C 464 PHE cc_start: 0.7944 (m-80) cc_final: 0.7724 (m-10) REVERT: C 619 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7755 (mm-30) outliers start: 22 outliers final: 8 residues processed: 389 average time/residue: 0.5287 time to fit residues: 240.4800 Evaluate side-chains 232 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 619 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 540 ASN A 641 ASN A1088 HIS A1113 GLN B 211 ASN C 81 ASN C 234 ASN C 388 ASN C 532 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145795 restraints weight = 29197.733| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.76 r_work: 0.3407 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24152 Z= 0.141 Angle : 0.655 10.042 32951 Z= 0.347 Chirality : 0.047 0.272 3878 Planarity : 0.004 0.035 4177 Dihedral : 7.153 74.865 3965 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 1.65 % Allowed : 7.90 % Favored : 90.44 % 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 are not related in a simple way. whole: 0.14 (0.15), residues: 2924 helix: 0.98 (0.20), residues: 664 sheet: 0.78 (0.18), residues: 693 loop : -0.59 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 577 TYR 0.021 0.002 TYR C 380 PHE 0.025 0.002 PHE A 58 TRP 0.017 0.002 TRP B 886 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00296 (24078) covalent geometry : angle 0.63514 (32766) SS BOND : bond 0.00506 ( 37) SS BOND : angle 1.37579 ( 74) hydrogen bonds : bond 0.05075 ( 1029) hydrogen bonds : angle 6.35383 ( 2841) link_BETA1-4 : bond 0.00834 ( 5) link_BETA1-4 : angle 1.93673 ( 15) link_NAG-ASN : bond 0.00422 ( 32) link_NAG-ASN : angle 2.78094 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8868 (p) cc_final: 0.8592 (t) REVERT: B 83 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7179 (p) REVERT: B 314 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 546 LEU cc_start: 0.7227 (tt) cc_final: 0.6879 (tp) REVERT: B 697 MET cc_start: 0.9285 (ptm) cc_final: 0.8942 (ptp) REVERT: B 935 GLN cc_start: 0.8426 (tt0) cc_final: 0.8178 (tt0) REVERT: C 52 GLN cc_start: 0.8675 (tp40) cc_final: 0.8214 (tp40) REVERT: C 453 PHE cc_start: 0.7123 (p90) cc_final: 0.6903 (p90) REVERT: C 619 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8196 (mp0) outliers start: 42 outliers final: 9 residues processed: 281 average time/residue: 0.4653 time to fit residues: 156.8044 Evaluate side-chains 202 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 290 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 641 ASN A 804 GLN B 394 ASN B 804 GLN B 955 ASN B1048 HIS C 81 ASN C 207 HIS C 388 ASN C 901 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.184247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142933 restraints weight = 29348.737| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.84 r_work: 0.3339 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24152 Z= 0.143 Angle : 0.584 9.542 32951 Z= 0.305 Chirality : 0.045 0.244 3878 Planarity : 0.004 0.047 4177 Dihedral : 6.473 74.623 3955 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.16 % Allowed : 9.52 % Favored : 88.32 % 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 are not related in a simple way. whole: 0.29 (0.15), residues: 2924 helix: 1.32 (0.20), residues: 673 sheet: 0.72 (0.18), residues: 700 loop : -0.55 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.025 0.002 TYR C 396 PHE 0.015 0.002 PHE B1121 TRP 0.013 0.002 TRP C 886 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00329 (24078) covalent geometry : angle 0.56768 (32766) SS BOND : bond 0.00498 ( 37) SS BOND : angle 1.47435 ( 74) hydrogen bonds : bond 0.04490 ( 1029) hydrogen bonds : angle 5.93922 ( 2841) link_BETA1-4 : bond 0.00468 ( 5) link_BETA1-4 : angle 1.55889 ( 15) link_NAG-ASN : bond 0.00335 ( 32) link_NAG-ASN : angle 2.21909 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8167 (mt) cc_final: 0.7862 (mp) REVERT: B 546 LEU cc_start: 0.7114 (tt) cc_final: 0.6849 (tp) REVERT: B 697 MET cc_start: 0.9338 (ptm) cc_final: 0.9082 (ptp) REVERT: B 878 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8411 (tt) REVERT: C 52 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8285 (tp40) REVERT: C 453 PHE cc_start: 0.7280 (p90) cc_final: 0.7016 (p90) REVERT: C 791 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 855 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: C 985 ASP cc_start: 0.7856 (p0) cc_final: 0.7537 (p0) REVERT: C 1010 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7727 (pt0) outliers start: 55 outliers final: 24 residues processed: 255 average time/residue: 0.4735 time to fit residues: 144.3279 Evaluate side-chains 216 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 86 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 170 optimal weight: 0.0670 chunk 157 optimal weight: 0.3980 chunk 255 optimal weight: 8.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN B 901 GLN C 165 ASN C 207 HIS C 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141425 restraints weight = 29103.131| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.82 r_work: 0.3313 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24152 Z= 0.198 Angle : 0.602 9.749 32951 Z= 0.313 Chirality : 0.047 0.228 3878 Planarity : 0.004 0.046 4177 Dihedral : 6.249 56.617 3952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.48 % Allowed : 11.09 % Favored : 86.43 % 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 are not related in a simple way. whole: 0.15 (0.15), residues: 2924 helix: 1.23 (0.20), residues: 675 sheet: 0.57 (0.18), residues: 688 loop : -0.60 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.030 0.002 TYR C 396 PHE 0.023 0.002 PHE C 342 TRP 0.012 0.002 TRP C 886 HIS 0.013 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00477 (24078) covalent geometry : angle 0.58730 (32766) SS BOND : bond 0.00469 ( 37) SS BOND : angle 1.61714 ( 74) hydrogen bonds : bond 0.04611 ( 1029) hydrogen bonds : angle 5.90214 ( 2841) link_BETA1-4 : bond 0.00403 ( 5) link_BETA1-4 : angle 1.32317 ( 15) link_NAG-ASN : bond 0.00346 ( 32) link_NAG-ASN : angle 2.09321 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ASP cc_start: 0.7399 (t0) cc_final: 0.6798 (m-30) REVERT: A 1045 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8198 (tttt) REVERT: B 128 ILE cc_start: 0.8267 (mt) cc_final: 0.8009 (mp) REVERT: B 646 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7713 (ttp80) REVERT: B 697 MET cc_start: 0.9384 (ptm) cc_final: 0.9114 (ptp) REVERT: B 878 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8398 (tt) REVERT: C 52 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8329 (tp40) REVERT: C 453 PHE cc_start: 0.7330 (p90) cc_final: 0.7071 (p90) REVERT: C 791 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 794 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7640 (pp) REVERT: C 855 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6948 (m-10) REVERT: C 985 ASP cc_start: 0.7723 (p0) cc_final: 0.7409 (p0) REVERT: C 1010 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (tt0) outliers start: 63 outliers final: 27 residues processed: 237 average time/residue: 0.4638 time to fit residues: 132.5248 Evaluate side-chains 215 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 212 optimal weight: 50.0000 chunk 181 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 556 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149007 restraints weight = 28963.310| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.62 r_work: 0.3309 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24152 Z= 0.158 Angle : 0.564 8.660 32951 Z= 0.293 Chirality : 0.045 0.221 3878 Planarity : 0.004 0.042 4177 Dihedral : 6.054 56.432 3952 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.67 % Allowed : 11.76 % Favored : 85.57 % 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 are not related in a simple way. whole: 0.19 (0.15), residues: 2924 helix: 1.40 (0.21), residues: 674 sheet: 0.55 (0.18), residues: 681 loop : -0.62 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.025 0.002 TYR C 396 PHE 0.028 0.001 PHE A 453 TRP 0.011 0.001 TRP A 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00373 (24078) covalent geometry : angle 0.55043 (32766) SS BOND : bond 0.00427 ( 37) SS BOND : angle 1.61733 ( 74) hydrogen bonds : bond 0.04256 ( 1029) hydrogen bonds : angle 5.73382 ( 2841) link_BETA1-4 : bond 0.00394 ( 5) link_BETA1-4 : angle 1.21554 ( 15) link_NAG-ASN : bond 0.00310 ( 32) link_NAG-ASN : angle 1.91718 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 PHE cc_start: 0.7983 (p90) cc_final: 0.7237 (p90) REVERT: A 808 ASP cc_start: 0.7361 (t0) cc_final: 0.6727 (m-30) REVERT: B 128 ILE cc_start: 0.7967 (mt) cc_final: 0.7595 (mp) REVERT: B 646 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7558 (ttp80) REVERT: B 697 MET cc_start: 0.9346 (ptm) cc_final: 0.9058 (ptp) REVERT: B 878 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8408 (tt) REVERT: C 52 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8577 (tp-100) REVERT: C 165 ASN cc_start: 0.3457 (OUTLIER) cc_final: 0.3132 (p0) REVERT: C 237 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7780 (mtp180) REVERT: C 453 PHE cc_start: 0.7273 (p90) cc_final: 0.6964 (p90) REVERT: C 791 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 796 ASP cc_start: 0.7154 (t0) cc_final: 0.6931 (t0) REVERT: C 855 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7069 (m-10) REVERT: C 985 ASP cc_start: 0.7673 (p0) cc_final: 0.7177 (p0) REVERT: C 1010 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7838 (pt0) outliers start: 68 outliers final: 33 residues processed: 233 average time/residue: 0.4409 time to fit residues: 124.8417 Evaluate side-chains 205 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 641 ASN A 804 GLN A1125 ASN B 207 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151006 restraints weight = 29020.535| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.60 r_work: 0.3292 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24152 Z= 0.111 Angle : 0.523 9.631 32951 Z= 0.273 Chirality : 0.044 0.206 3878 Planarity : 0.004 0.076 4177 Dihedral : 5.773 55.817 3952 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.12 % Allowed : 12.82 % Favored : 85.06 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 2924 helix: 1.66 (0.21), residues: 675 sheet: 0.56 (0.19), residues: 667 loop : -0.56 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.029 0.001 TYR A 508 PHE 0.022 0.001 PHE A 453 TRP 0.015 0.001 TRP A 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00244 (24078) covalent geometry : angle 0.51080 (32766) SS BOND : bond 0.00322 ( 37) SS BOND : angle 1.42836 ( 74) hydrogen bonds : bond 0.03782 ( 1029) hydrogen bonds : angle 5.49358 ( 2841) link_BETA1-4 : bond 0.00511 ( 5) link_BETA1-4 : angle 1.18849 ( 15) link_NAG-ASN : bond 0.00310 ( 32) link_NAG-ASN : angle 1.69445 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6209 (OUTLIER) cc_final: 0.5930 (p0) REVERT: A 453 PHE cc_start: 0.7518 (p90) cc_final: 0.6673 (p90) REVERT: A 808 ASP cc_start: 0.7285 (t0) cc_final: 0.6681 (m-30) REVERT: A 1045 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8190 (tttt) REVERT: B 128 ILE cc_start: 0.7603 (mt) cc_final: 0.7238 (mp) REVERT: B 326 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7422 (tt) REVERT: B 584 ILE cc_start: 0.8705 (mt) cc_final: 0.8488 (mm) REVERT: B 697 MET cc_start: 0.9318 (ptm) cc_final: 0.8987 (ptp) REVERT: B 878 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (tt) REVERT: C 237 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7827 (mtp180) REVERT: C 453 PHE cc_start: 0.6848 (p90) cc_final: 0.6610 (p90) REVERT: C 619 GLU cc_start: 0.8427 (mp0) cc_final: 0.8161 (mm-30) REVERT: C 855 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: C 1010 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: C 1073 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8024 (ttpt) outliers start: 54 outliers final: 27 residues processed: 236 average time/residue: 0.4567 time to fit residues: 129.8077 Evaluate side-chains 214 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 0.1980 chunk 290 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 169 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 556 ASN A 641 ASN A1125 ASN B 207 HIS B 354 ASN B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153467 restraints weight = 28999.016| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.54 r_work: 0.3328 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24152 Z= 0.093 Angle : 0.503 10.245 32951 Z= 0.258 Chirality : 0.043 0.193 3878 Planarity : 0.004 0.059 4177 Dihedral : 5.462 55.188 3952 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.65 % Allowed : 13.53 % Favored : 84.82 % 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 are not related in a simple way. whole: 0.53 (0.15), residues: 2924 helix: 1.94 (0.21), residues: 670 sheet: 0.53 (0.19), residues: 667 loop : -0.39 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.030 0.001 TYR A 508 PHE 0.023 0.001 PHE A 453 TRP 0.023 0.001 TRP A 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00197 (24078) covalent geometry : angle 0.49466 (32766) SS BOND : bond 0.00300 ( 37) SS BOND : angle 1.14292 ( 74) hydrogen bonds : bond 0.03440 ( 1029) hydrogen bonds : angle 5.25470 ( 2841) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 1.15182 ( 15) link_NAG-ASN : bond 0.00309 ( 32) link_NAG-ASN : angle 1.49626 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8074 (t80) cc_final: 0.7860 (t80) REVERT: A 675 GLN cc_start: 0.7313 (tp40) cc_final: 0.7079 (mm110) REVERT: A 808 ASP cc_start: 0.7426 (t0) cc_final: 0.7190 (t0) REVERT: B 128 ILE cc_start: 0.7593 (mt) cc_final: 0.7172 (mp) REVERT: B 326 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7472 (tt) REVERT: B 584 ILE cc_start: 0.8608 (mt) cc_final: 0.8402 (mm) REVERT: B 697 MET cc_start: 0.9311 (ptm) cc_final: 0.9050 (ptp) REVERT: B 878 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8429 (tt) REVERT: C 619 GLU cc_start: 0.8395 (mp0) cc_final: 0.8139 (mm-30) REVERT: C 855 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6828 (m-10) REVERT: C 1010 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: C 1073 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7982 (ttpt) outliers start: 42 outliers final: 19 residues processed: 227 average time/residue: 0.4300 time to fit residues: 119.4968 Evaluate side-chains 199 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS C 360 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148325 restraints weight = 28962.297| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.62 r_work: 0.3248 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24152 Z= 0.230 Angle : 0.600 12.172 32951 Z= 0.307 Chirality : 0.047 0.226 3878 Planarity : 0.004 0.069 4177 Dihedral : 5.818 56.279 3952 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.04 % Allowed : 13.84 % Favored : 84.11 % 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 are not related in a simple way. whole: 0.25 (0.15), residues: 2924 helix: 1.52 (0.21), residues: 666 sheet: 0.47 (0.19), residues: 677 loop : -0.53 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.026 0.002 TYR A 508 PHE 0.031 0.002 PHE C 453 TRP 0.021 0.002 TRP A 104 HIS 0.011 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00557 (24078) covalent geometry : angle 0.58793 (32766) SS BOND : bond 0.00563 ( 37) SS BOND : angle 1.62641 ( 74) hydrogen bonds : bond 0.04440 ( 1029) hydrogen bonds : angle 5.54166 ( 2841) link_BETA1-4 : bond 0.00296 ( 5) link_BETA1-4 : angle 1.11423 ( 15) link_NAG-ASN : bond 0.00302 ( 32) link_NAG-ASN : angle 1.83665 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 PHE cc_start: 0.7503 (p90) cc_final: 0.6883 (p90) REVERT: A 558 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7456 (mmmt) REVERT: A 675 GLN cc_start: 0.7375 (tp40) cc_final: 0.7148 (mm110) REVERT: A 808 ASP cc_start: 0.7388 (t0) cc_final: 0.6816 (m-30) REVERT: A 1045 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8218 (tttt) REVERT: B 128 ILE cc_start: 0.7615 (mt) cc_final: 0.7171 (mp) REVERT: B 546 LEU cc_start: 0.7051 (tt) cc_final: 0.6784 (tp) REVERT: B 697 MET cc_start: 0.9340 (ptm) cc_final: 0.9064 (ptp) REVERT: B 878 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 52 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8548 (tp-100) REVERT: C 239 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7327 (mm-40) REVERT: C 619 GLU cc_start: 0.8551 (mp0) cc_final: 0.8292 (mm-30) REVERT: C 791 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 855 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: C 1010 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 1073 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8115 (ttpt) outliers start: 52 outliers final: 32 residues processed: 223 average time/residue: 0.4663 time to fit residues: 124.2422 Evaluate side-chains 213 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 274 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 556 ASN A 641 ASN A1125 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145007 restraints weight = 29089.249| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.76 r_work: 0.3380 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24152 Z= 0.131 Angle : 0.538 9.876 32951 Z= 0.275 Chirality : 0.044 0.201 3878 Planarity : 0.004 0.061 4177 Dihedral : 5.635 55.560 3952 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 14.24 % Favored : 83.96 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 2924 helix: 1.64 (0.21), residues: 673 sheet: 0.46 (0.19), residues: 651 loop : -0.48 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.022 0.001 TYR B1138 PHE 0.033 0.001 PHE C 453 TRP 0.027 0.001 TRP A 104 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (24078) covalent geometry : angle 0.52771 (32766) SS BOND : bond 0.00351 ( 37) SS BOND : angle 1.33330 ( 74) hydrogen bonds : bond 0.03844 ( 1029) hydrogen bonds : angle 5.37508 ( 2841) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.09058 ( 15) link_NAG-ASN : bond 0.00271 ( 32) link_NAG-ASN : angle 1.63622 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 PHE cc_start: 0.7886 (p90) cc_final: 0.7402 (p90) REVERT: A 675 GLN cc_start: 0.7146 (tp40) cc_final: 0.6923 (mm110) REVERT: A 808 ASP cc_start: 0.7310 (t0) cc_final: 0.6799 (m-30) REVERT: A 1045 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8122 (tttt) REVERT: B 697 MET cc_start: 0.9301 (ptm) cc_final: 0.9022 (ptp) REVERT: B 878 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8345 (tt) REVERT: C 239 GLN cc_start: 0.7322 (tp-100) cc_final: 0.7084 (mm-40) REVERT: C 619 GLU cc_start: 0.8392 (mp0) cc_final: 0.8086 (mm-30) REVERT: C 796 ASP cc_start: 0.7106 (t0) cc_final: 0.6880 (t0) REVERT: C 855 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: C 1010 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: C 1073 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7888 (ttpt) outliers start: 46 outliers final: 32 residues processed: 219 average time/residue: 0.4384 time to fit residues: 115.6906 Evaluate side-chains 208 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 165 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 183 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 556 ASN A 641 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS C 360 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.184859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144645 restraints weight = 28999.816| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.81 r_work: 0.3343 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24152 Z= 0.110 Angle : 0.531 11.101 32951 Z= 0.272 Chirality : 0.044 0.274 3878 Planarity : 0.004 0.055 4177 Dihedral : 5.536 55.246 3952 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.45 % Allowed : 14.83 % Favored : 83.72 % 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 are not related in a simple way. whole: 0.41 (0.15), residues: 2924 helix: 1.83 (0.21), residues: 667 sheet: 0.43 (0.19), residues: 645 loop : -0.43 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.020 0.001 TYR C 170 PHE 0.033 0.001 PHE C 453 TRP 0.035 0.001 TRP A 104 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00249 (24078) covalent geometry : angle 0.52084 (32766) SS BOND : bond 0.00378 ( 37) SS BOND : angle 1.42608 ( 74) hydrogen bonds : bond 0.03671 ( 1029) hydrogen bonds : angle 5.30722 ( 2841) link_BETA1-4 : bond 0.00426 ( 5) link_BETA1-4 : angle 1.08358 ( 15) link_NAG-ASN : bond 0.00324 ( 32) link_NAG-ASN : angle 1.61251 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 PHE cc_start: 0.7905 (p90) cc_final: 0.7395 (p90) REVERT: A 675 GLN cc_start: 0.7087 (tp40) cc_final: 0.6882 (mm110) REVERT: A 808 ASP cc_start: 0.7239 (t0) cc_final: 0.6762 (m-30) REVERT: A 1045 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7907 (tttt) REVERT: B 128 ILE cc_start: 0.8058 (mt) cc_final: 0.7741 (mp) REVERT: B 697 MET cc_start: 0.9171 (ptm) cc_final: 0.8956 (ptp) REVERT: B 878 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8274 (tt) REVERT: C 239 GLN cc_start: 0.7267 (tp-100) cc_final: 0.7027 (mm-40) REVERT: C 619 GLU cc_start: 0.8306 (mp0) cc_final: 0.7999 (mm-30) REVERT: C 855 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7042 (m-10) REVERT: C 1010 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7668 (pt0) REVERT: C 1073 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7639 (ttpt) outliers start: 37 outliers final: 28 residues processed: 206 average time/residue: 0.4421 time to fit residues: 110.0215 Evaluate side-chains 209 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 155 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 156 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 556 ASN A 641 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 165 ASN C 207 HIS C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144286 restraints weight = 28988.985| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.83 r_work: 0.3335 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24152 Z= 0.106 Angle : 0.521 11.311 32951 Z= 0.266 Chirality : 0.043 0.221 3878 Planarity : 0.004 0.061 4177 Dihedral : 5.438 55.086 3952 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.61 % Allowed : 14.51 % Favored : 83.88 % 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 are not related in a simple way. whole: 0.49 (0.15), residues: 2924 helix: 1.90 (0.21), residues: 668 sheet: 0.43 (0.19), residues: 655 loop : -0.36 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 466 TYR 0.022 0.001 TYR B 170 PHE 0.034 0.001 PHE C 453 TRP 0.040 0.001 TRP A 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (24078) covalent geometry : angle 0.51192 (32766) SS BOND : bond 0.00301 ( 37) SS BOND : angle 1.29669 ( 74) hydrogen bonds : bond 0.03559 ( 1029) hydrogen bonds : angle 5.22287 ( 2841) link_BETA1-4 : bond 0.00428 ( 5) link_BETA1-4 : angle 1.08240 ( 15) link_NAG-ASN : bond 0.00285 ( 32) link_NAG-ASN : angle 1.52077 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6793.36 seconds wall clock time: 116 minutes 30.79 seconds (6990.79 seconds total)