Starting phenix.real_space_refine on Mon Aug 25 10:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhx_34806/08_2025/8hhx_34806.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17425 2.51 5 N 4532 2.21 5 O 5358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27435 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6373 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 39, 'TRANS': 782} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7646 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 931} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1682 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "G" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1614 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 831 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" 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: "L" 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: "P" 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: "U" 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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 Time building chain proxies: 6.86, per 1000 atoms: 0.25 Number of scatterers: 27435 At special positions: 0 Unit cell: (161.85, 174.3, 185.92, 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 120 16.00 O 5358 8.00 N 4532 7.00 C 17425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 216 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG D 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG P 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 63 sheets defined 21.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.996A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.997A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.549A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.847A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.755A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.980A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.797A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.869A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.937A pdb=" N SER B 373 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.597A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.798A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.632A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.560A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.200A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.549A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.445A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.386A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.665A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.501A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.558A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.930A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.429A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.977A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.526A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.238A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.530A pdb=" N GLU G 129 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.989A pdb=" N ASN G 175 " --> pdb=" O GLN G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 193 removed outlier: 4.198A pdb=" N TRP G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS G 193 " --> pdb=" O GLN G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.695A pdb=" N ASN I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.652A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.777A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 205 removed outlier: 6.358A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N VAL A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.305A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.931A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.051A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.568A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.977A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 removed outlier: 5.897A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.218A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.818A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.818A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.586A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.201A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.860A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.745A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.948A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.662A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.748A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 396 removed outlier: 3.715A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.506A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.104A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1053 through 1056 removed outlier: 3.653A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1089 through 1090 removed outlier: 3.531A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.077A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 95 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS F 96 " --> pdb=" O TRP F 111 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP F 111 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN F 98 " --> pdb=" O ASP F 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.512A pdb=" N VAL F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 59 " --> pdb=" O VAL F 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AG2, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.539A pdb=" N ALA G 75 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 74 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP G 69 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 76 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 67 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.900A pdb=" N VAL G 49 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 38 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 91 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AG5, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AG6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AG7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.840A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.660A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.608A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2085 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: 5.96 Time building geometry restraints manager: 3.09 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: 7410 1.33 - 1.46: 6924 1.46 - 1.58: 13562 1.58 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 28051 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CB PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.79e+00 bond pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 ... (remaining 28046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 37882 2.88 - 5.77: 261 5.77 - 8.65: 22 8.65 - 11.53: 5 11.53 - 14.41: 1 Bond angle restraints: 38171 Sorted by residual: angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 97.59 14.41 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 95.22 7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C ASP A 737 " pdb=" CA ASP A 737 " pdb=" CB ASP A 737 " ideal model delta sigma weight residual 110.77 118.42 -7.65 1.67e+00 3.59e-01 2.10e+01 angle pdb=" N GLN C 954 " pdb=" CA GLN C 954 " pdb=" CB GLN C 954 " ideal model delta sigma weight residual 110.32 117.74 -7.42 1.70e+00 3.46e-01 1.90e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" CB GLN A 774 " ideal model delta sigma weight residual 110.12 116.37 -6.25 1.47e+00 4.63e-01 1.81e+01 ... (remaining 38166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 16284 24.86 - 49.72: 739 49.72 - 74.59: 88 74.59 - 99.45: 20 99.45 - 124.31: 1 Dihedral angle restraints: 17132 sinusoidal: 7034 harmonic: 10098 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.92 78.92 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 17129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4430 0.190 - 0.380: 4 0.380 - 0.570: 0 0.570 - 0.760: 1 0.760 - 0.950: 1 Chirality restraints: 4436 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4433 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.098 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 272 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.091 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO C 272 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.049 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN A 616 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.051 2.00e-02 2.50e+03 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 557 2.67 - 3.23: 26207 3.23 - 3.79: 40161 3.79 - 4.34: 53517 4.34 - 4.90: 86634 Nonbonded interactions: 207076 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.114 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.144 3.040 nonbonded pdb=" O THR B 961 " pdb=" OE1 GLN B 965 " model vdw 2.151 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B1067 " pdb=" O ASN B1108 " model vdw 2.197 3.040 ... (remaining 207071 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 'B' and (resid 25 through 146 or resid 164 through 165 or resid 186 throu \ gh 463 or resid 491 through 1307)) selection = (chain 'C' and (resid 25 through 69 or resid 81 through 146 or resid 148 through \ 149 or resid 186 through 243 or resid 264 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.590 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 28122 Z= 0.187 Angle : 0.664 18.597 38348 Z= 0.345 Chirality : 0.050 0.950 4436 Planarity : 0.005 0.146 4881 Dihedral : 13.430 124.309 10534 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 624 sheet: -0.85 (0.23), residues: 535 loop : -1.13 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.021 0.001 TYR A 873 PHE 0.024 0.001 PHE C1103 TRP 0.025 0.001 TRP B 353 HIS 0.014 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00378 (28051) covalent geometry : angle 0.63726 (38171) SS BOND : bond 0.00408 ( 36) SS BOND : angle 1.27540 ( 72) hydrogen bonds : bond 0.21112 ( 766) hydrogen bonds : angle 9.57611 ( 2085) link_BETA1-4 : bond 0.00557 ( 7) link_BETA1-4 : angle 1.47726 ( 21) link_NAG-ASN : bond 0.00658 ( 28) link_NAG-ASN : angle 3.82678 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 414 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 ASP cc_start: 0.5105 (t70) cc_final: 0.4795 (t70) outliers start: 5 outliers final: 2 residues processed: 418 average time/residue: 0.1751 time to fit residues: 118.8077 Evaluate side-chains 326 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 164 ASN B 540 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN G 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.249874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.216643 restraints weight = 43555.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217158 restraints weight = 48565.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.217670 restraints weight = 43436.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.218094 restraints weight = 24981.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.219412 restraints weight = 21352.384| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28122 Z= 0.161 Angle : 0.628 9.757 38348 Z= 0.324 Chirality : 0.047 0.342 4436 Planarity : 0.005 0.107 4881 Dihedral : 7.085 109.993 4457 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.06 % Allowed : 7.31 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.14), residues: 3419 helix: 0.31 (0.21), residues: 618 sheet: -0.67 (0.22), residues: 574 loop : -1.19 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.020 0.001 TYR A1110 PHE 0.018 0.001 PHE B 275 TRP 0.021 0.001 TRP B 353 HIS 0.011 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00358 (28051) covalent geometry : angle 0.61177 (38171) SS BOND : bond 0.00513 ( 36) SS BOND : angle 1.19714 ( 72) hydrogen bonds : bond 0.05105 ( 766) hydrogen bonds : angle 7.36192 ( 2085) link_BETA1-4 : bond 0.00634 ( 7) link_BETA1-4 : angle 1.25717 ( 21) link_NAG-ASN : bond 0.00609 ( 28) link_NAG-ASN : angle 2.85423 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 818 ILE cc_start: 0.7467 (mp) cc_final: 0.6861 (mt) REVERT: F 57 ASN cc_start: 0.5806 (p0) cc_final: 0.5419 (p0) outliers start: 32 outliers final: 20 residues processed: 391 average time/residue: 0.1722 time to fit residues: 109.6142 Evaluate side-chains 356 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 30 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.245774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.211132 restraints weight = 43512.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.210115 restraints weight = 50517.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.211911 restraints weight = 40370.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.212183 restraints weight = 24046.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.213740 restraints weight = 21262.813| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28122 Z= 0.232 Angle : 0.686 11.594 38348 Z= 0.354 Chirality : 0.048 0.371 4436 Planarity : 0.005 0.082 4881 Dihedral : 7.053 106.716 4455 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.60 % Favored : 92.37 % Rotamer: Outliers : 2.19 % Allowed : 10.80 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.14), residues: 3419 helix: -0.02 (0.20), residues: 613 sheet: -0.89 (0.23), residues: 530 loop : -1.35 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1014 TYR 0.023 0.002 TYR A1067 PHE 0.023 0.002 PHE A 192 TRP 0.026 0.002 TRP B 353 HIS 0.013 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00528 (28051) covalent geometry : angle 0.67194 (38171) SS BOND : bond 0.00493 ( 36) SS BOND : angle 1.29773 ( 72) hydrogen bonds : bond 0.05373 ( 766) hydrogen bonds : angle 7.21914 ( 2085) link_BETA1-4 : bond 0.00600 ( 7) link_BETA1-4 : angle 1.46358 ( 21) link_NAG-ASN : bond 0.00606 ( 28) link_NAG-ASN : angle 2.82539 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 357 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4573 (OUTLIER) cc_final: 0.4259 (mp0) REVERT: A 906 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: B 347 PHE cc_start: 0.4025 (m-80) cc_final: 0.3658 (m-10) REVERT: B 900 MET cc_start: 0.6894 (mmt) cc_final: 0.6630 (mmt) REVERT: C 716 THR cc_start: 0.7308 (p) cc_final: 0.6970 (t) REVERT: C 818 ILE cc_start: 0.7664 (mp) cc_final: 0.7436 (mt) REVERT: C 949 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6688 (tp-100) REVERT: C 1106 GLN cc_start: 0.7640 (pm20) cc_final: 0.6894 (pm20) REVERT: F 57 ASN cc_start: 0.5797 (p0) cc_final: 0.5362 (p0) outliers start: 66 outliers final: 43 residues processed: 400 average time/residue: 0.1604 time to fit residues: 104.4775 Evaluate side-chains 368 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 330 optimal weight: 5.9990 chunk 232 optimal weight: 0.1980 chunk 326 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 258 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1113 GLN G 39 GLN G 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.248382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.214055 restraints weight = 42978.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.214536 restraints weight = 41965.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.215519 restraints weight = 36103.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.216050 restraints weight = 22071.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.216748 restraints weight = 19606.619| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28122 Z= 0.151 Angle : 0.609 12.056 38348 Z= 0.312 Chirality : 0.047 0.342 4436 Planarity : 0.004 0.072 4881 Dihedral : 6.659 105.303 4455 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.26 % Allowed : 12.97 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.14), residues: 3419 helix: 0.14 (0.20), residues: 619 sheet: -0.80 (0.23), residues: 550 loop : -1.30 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.018 0.001 TYR B 170 PHE 0.013 0.001 PHE B 201 TRP 0.026 0.001 TRP B 353 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00338 (28051) covalent geometry : angle 0.59447 (38171) SS BOND : bond 0.00285 ( 36) SS BOND : angle 1.09164 ( 72) hydrogen bonds : bond 0.04730 ( 766) hydrogen bonds : angle 6.81838 ( 2085) link_BETA1-4 : bond 0.00527 ( 7) link_BETA1-4 : angle 1.31702 ( 21) link_NAG-ASN : bond 0.00611 ( 28) link_NAG-ASN : angle 2.69566 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4281 (OUTLIER) cc_final: 0.3978 (mp0) REVERT: A 660 TYR cc_start: 0.6724 (p90) cc_final: 0.6338 (p90) REVERT: A 906 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: B 900 MET cc_start: 0.6871 (mmt) cc_final: 0.6552 (mmt) REVERT: C 818 ILE cc_start: 0.7539 (mp) cc_final: 0.6954 (mt) REVERT: C 886 TRP cc_start: 0.6509 (p90) cc_final: 0.5482 (p90) REVERT: C 1106 GLN cc_start: 0.7635 (pm20) cc_final: 0.6865 (pm20) REVERT: F 57 ASN cc_start: 0.5960 (p0) cc_final: 0.5497 (p0) outliers start: 68 outliers final: 50 residues processed: 399 average time/residue: 0.1443 time to fit residues: 95.3505 Evaluate side-chains 374 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 322 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 264 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 913 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 536 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.246164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.211034 restraints weight = 43085.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.211329 restraints weight = 43165.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.212475 restraints weight = 36290.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.212826 restraints weight = 21903.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213578 restraints weight = 19704.110| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28122 Z= 0.177 Angle : 0.627 11.873 38348 Z= 0.322 Chirality : 0.047 0.359 4436 Planarity : 0.005 0.063 4881 Dihedral : 6.530 103.225 4455 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.69 % Allowed : 14.06 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.14), residues: 3419 helix: 0.12 (0.20), residues: 617 sheet: -0.93 (0.22), residues: 570 loop : -1.35 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.017 0.001 TYR A1067 PHE 0.019 0.001 PHE A 192 TRP 0.028 0.001 TRP B 353 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00402 (28051) covalent geometry : angle 0.61381 (38171) SS BOND : bond 0.00356 ( 36) SS BOND : angle 0.99007 ( 72) hydrogen bonds : bond 0.04810 ( 766) hydrogen bonds : angle 6.75702 ( 2085) link_BETA1-4 : bond 0.00500 ( 7) link_BETA1-4 : angle 1.32617 ( 21) link_NAG-ASN : bond 0.00584 ( 28) link_NAG-ASN : angle 2.62957 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 343 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4237 (OUTLIER) cc_final: 0.3932 (mp0) REVERT: A 660 TYR cc_start: 0.6692 (p90) cc_final: 0.6473 (p90) REVERT: B 347 PHE cc_start: 0.4125 (m-80) cc_final: 0.3692 (m-10) REVERT: B 900 MET cc_start: 0.6852 (mmt) cc_final: 0.6549 (mmt) REVERT: C 716 THR cc_start: 0.7215 (p) cc_final: 0.6962 (t) REVERT: C 721 SER cc_start: 0.8333 (t) cc_final: 0.8108 (m) REVERT: C 818 ILE cc_start: 0.7528 (mp) cc_final: 0.6968 (mt) REVERT: C 1106 GLN cc_start: 0.7736 (pm20) cc_final: 0.6906 (pm20) REVERT: F 57 ASN cc_start: 0.5845 (p0) cc_final: 0.5448 (p0) outliers start: 81 outliers final: 53 residues processed: 400 average time/residue: 0.1601 time to fit residues: 104.7829 Evaluate side-chains 384 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 215 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 155 optimal weight: 0.1980 chunk 326 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.246054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.210642 restraints weight = 43660.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.208674 restraints weight = 46180.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.210136 restraints weight = 43533.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.210697 restraints weight = 24562.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.211645 restraints weight = 20839.348| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28122 Z= 0.192 Angle : 0.649 12.076 38348 Z= 0.334 Chirality : 0.048 0.409 4436 Planarity : 0.005 0.064 4881 Dihedral : 6.482 101.065 4455 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.86 % Allowed : 14.93 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3419 helix: 0.02 (0.20), residues: 626 sheet: -1.08 (0.22), residues: 582 loop : -1.38 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 983 TYR 0.018 0.002 TYR A1067 PHE 0.023 0.002 PHE A 192 TRP 0.027 0.001 TRP B 353 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00439 (28051) covalent geometry : angle 0.63643 (38171) SS BOND : bond 0.00351 ( 36) SS BOND : angle 1.09197 ( 72) hydrogen bonds : bond 0.04957 ( 766) hydrogen bonds : angle 6.76919 ( 2085) link_BETA1-4 : bond 0.00505 ( 7) link_BETA1-4 : angle 1.38352 ( 21) link_NAG-ASN : bond 0.00587 ( 28) link_NAG-ASN : angle 2.62140 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 353 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4168 (OUTLIER) cc_final: 0.3816 (mp0) REVERT: A 660 TYR cc_start: 0.6861 (p90) cc_final: 0.6633 (p90) REVERT: B 347 PHE cc_start: 0.4293 (m-80) cc_final: 0.3874 (m-10) REVERT: B 900 MET cc_start: 0.7027 (mmt) cc_final: 0.6728 (mmt) REVERT: C 143 VAL cc_start: -0.0723 (OUTLIER) cc_final: -0.1052 (p) REVERT: C 716 THR cc_start: 0.7276 (p) cc_final: 0.7006 (t) REVERT: C 721 SER cc_start: 0.8425 (t) cc_final: 0.8194 (m) REVERT: C 818 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7053 (mt) REVERT: C 900 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6185 (mmm) REVERT: F 57 ASN cc_start: 0.5821 (p0) cc_final: 0.5452 (p0) outliers start: 86 outliers final: 66 residues processed: 409 average time/residue: 0.1685 time to fit residues: 114.0376 Evaluate side-chains 401 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 331 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 126 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 312 optimal weight: 20.0000 chunk 54 optimal weight: 0.0870 chunk 247 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 overall best weight: 2.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 965 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.244794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.209397 restraints weight = 42994.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.209508 restraints weight = 43974.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.210265 restraints weight = 38787.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.210601 restraints weight = 22285.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.211802 restraints weight = 18970.579| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28122 Z= 0.193 Angle : 0.659 12.641 38348 Z= 0.339 Chirality : 0.048 0.403 4436 Planarity : 0.005 0.064 4881 Dihedral : 6.413 99.583 4455 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.09 % Allowed : 15.92 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.14), residues: 3419 helix: -0.09 (0.20), residues: 626 sheet: -1.09 (0.22), residues: 590 loop : -1.40 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 765 TYR 0.018 0.002 TYR C 91 PHE 0.030 0.002 PHE C 718 TRP 0.026 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00438 (28051) covalent geometry : angle 0.64597 (38171) SS BOND : bond 0.00501 ( 36) SS BOND : angle 1.27318 ( 72) hydrogen bonds : bond 0.05007 ( 766) hydrogen bonds : angle 6.78524 ( 2085) link_BETA1-4 : bond 0.00520 ( 7) link_BETA1-4 : angle 1.39471 ( 21) link_NAG-ASN : bond 0.00580 ( 28) link_NAG-ASN : angle 2.60291 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 350 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4161 (OUTLIER) cc_final: 0.3797 (mp0) REVERT: B 347 PHE cc_start: 0.4317 (m-80) cc_final: 0.3914 (m-10) REVERT: B 900 MET cc_start: 0.6991 (mmt) cc_final: 0.6688 (mmt) REVERT: B 1029 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.4951 (ttm) REVERT: C 143 VAL cc_start: -0.0711 (OUTLIER) cc_final: -0.1037 (p) REVERT: C 716 THR cc_start: 0.7355 (p) cc_final: 0.7048 (t) REVERT: C 721 SER cc_start: 0.8398 (t) cc_final: 0.8149 (m) REVERT: C 900 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.6212 (mmm) REVERT: F 57 ASN cc_start: 0.5927 (p0) cc_final: 0.5538 (p0) outliers start: 93 outliers final: 71 residues processed: 414 average time/residue: 0.1607 time to fit residues: 110.4340 Evaluate side-chains 401 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 326 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 317 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 141 optimal weight: 0.1980 chunk 210 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.248383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.213304 restraints weight = 43192.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.213379 restraints weight = 40233.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.214147 restraints weight = 34422.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.214501 restraints weight = 20949.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.215814 restraints weight = 17544.525| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28122 Z= 0.126 Angle : 0.623 14.436 38348 Z= 0.318 Chirality : 0.047 0.366 4436 Planarity : 0.004 0.062 4881 Dihedral : 6.014 98.313 4455 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.56 % Allowed : 16.72 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.14), residues: 3419 helix: 0.04 (0.20), residues: 620 sheet: -0.97 (0.22), residues: 595 loop : -1.27 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.018 0.001 TYR A1110 PHE 0.018 0.001 PHE C 718 TRP 0.024 0.001 TRP B 353 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00280 (28051) covalent geometry : angle 0.61033 (38171) SS BOND : bond 0.00280 ( 36) SS BOND : angle 1.12027 ( 72) hydrogen bonds : bond 0.04398 ( 766) hydrogen bonds : angle 6.47773 ( 2085) link_BETA1-4 : bond 0.00557 ( 7) link_BETA1-4 : angle 1.41311 ( 21) link_NAG-ASN : bond 0.00526 ( 28) link_NAG-ASN : angle 2.47146 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 PHE cc_start: 0.4266 (m-80) cc_final: 0.3888 (m-10) REVERT: B 900 MET cc_start: 0.6951 (mmt) cc_final: 0.6714 (mmt) REVERT: C 716 THR cc_start: 0.7223 (p) cc_final: 0.6960 (t) REVERT: C 721 SER cc_start: 0.8157 (t) cc_final: 0.7932 (m) REVERT: C 900 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.6021 (mmm) REVERT: C 964 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7396 (mtmm) REVERT: C 1106 GLN cc_start: 0.7736 (pm20) cc_final: 0.6930 (pm20) REVERT: F 57 ASN cc_start: 0.6003 (p0) cc_final: 0.5562 (p0) REVERT: G 183 LEU cc_start: 0.1383 (OUTLIER) cc_final: 0.1027 (pt) outliers start: 77 outliers final: 60 residues processed: 426 average time/residue: 0.1667 time to fit residues: 117.2734 Evaluate side-chains 397 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 1 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 198 optimal weight: 0.2980 chunk 329 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 895 GLN A1010 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.245682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.211009 restraints weight = 43099.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.210904 restraints weight = 45725.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.212275 restraints weight = 37599.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.212573 restraints weight = 23430.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213688 restraints weight = 21104.632| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28122 Z= 0.176 Angle : 0.661 13.505 38348 Z= 0.339 Chirality : 0.048 0.371 4436 Planarity : 0.005 0.064 4881 Dihedral : 6.032 95.320 4455 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.66 % Allowed : 16.92 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3419 helix: -0.03 (0.20), residues: 632 sheet: -0.96 (0.22), residues: 585 loop : -1.35 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.016 0.001 TYR B 170 PHE 0.029 0.002 PHE C1103 TRP 0.022 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00401 (28051) covalent geometry : angle 0.64920 (38171) SS BOND : bond 0.00366 ( 36) SS BOND : angle 1.13662 ( 72) hydrogen bonds : bond 0.04743 ( 766) hydrogen bonds : angle 6.59330 ( 2085) link_BETA1-4 : bond 0.00514 ( 7) link_BETA1-4 : angle 1.32464 ( 21) link_NAG-ASN : bond 0.00554 ( 28) link_NAG-ASN : angle 2.51753 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 TYR cc_start: 0.6895 (p90) cc_final: 0.6569 (p90) REVERT: B 347 PHE cc_start: 0.4315 (m-80) cc_final: 0.3942 (m-10) REVERT: B 1029 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.5028 (ttm) REVERT: C 716 THR cc_start: 0.7284 (p) cc_final: 0.7041 (t) REVERT: C 721 SER cc_start: 0.8160 (t) cc_final: 0.7922 (m) REVERT: C 900 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.6023 (mmm) REVERT: F 57 ASN cc_start: 0.5996 (p0) cc_final: 0.5592 (p0) REVERT: G 183 LEU cc_start: 0.1495 (OUTLIER) cc_final: 0.1065 (pt) outliers start: 80 outliers final: 66 residues processed: 408 average time/residue: 0.1684 time to fit residues: 114.1028 Evaluate side-chains 404 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 116 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 120 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 710 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.246744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.213543 restraints weight = 43847.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.211487 restraints weight = 60893.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213723 restraints weight = 48915.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213969 restraints weight = 28552.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214745 restraints weight = 26997.264| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28122 Z= 0.168 Angle : 0.662 13.933 38348 Z= 0.340 Chirality : 0.048 0.384 4436 Planarity : 0.005 0.068 4881 Dihedral : 5.965 94.060 4452 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.59 % Allowed : 17.25 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.14), residues: 3419 helix: -0.07 (0.20), residues: 630 sheet: -0.97 (0.22), residues: 587 loop : -1.35 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.014 0.001 TYR A1067 PHE 0.018 0.001 PHE C 718 TRP 0.022 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00383 (28051) covalent geometry : angle 0.65104 (38171) SS BOND : bond 0.00335 ( 36) SS BOND : angle 1.16201 ( 72) hydrogen bonds : bond 0.04741 ( 766) hydrogen bonds : angle 6.57612 ( 2085) link_BETA1-4 : bond 0.00514 ( 7) link_BETA1-4 : angle 1.33716 ( 21) link_NAG-ASN : bond 0.00537 ( 28) link_NAG-ASN : angle 2.47187 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 339 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 TYR cc_start: 0.6920 (p90) cc_final: 0.6645 (p90) REVERT: B 347 PHE cc_start: 0.4332 (m-80) cc_final: 0.3956 (m-10) REVERT: B 1029 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4957 (ttm) REVERT: C 716 THR cc_start: 0.7249 (p) cc_final: 0.7006 (t) REVERT: C 721 SER cc_start: 0.8297 (t) cc_final: 0.7929 (m) REVERT: C 900 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.6020 (mmm) REVERT: F 57 ASN cc_start: 0.5994 (p0) cc_final: 0.5597 (p0) REVERT: G 183 LEU cc_start: 0.1470 (OUTLIER) cc_final: 0.1029 (pt) outliers start: 78 outliers final: 68 residues processed: 391 average time/residue: 0.1485 time to fit residues: 97.3257 Evaluate side-chains 407 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 336 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 280 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 394 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.245590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.210623 restraints weight = 42912.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.210879 restraints weight = 42969.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.211941 restraints weight = 38661.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.212301 restraints weight = 23691.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.213359 restraints weight = 20852.493| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28122 Z= 0.178 Angle : 0.679 14.034 38348 Z= 0.346 Chirality : 0.049 0.394 4436 Planarity : 0.005 0.065 4881 Dihedral : 5.969 91.668 4452 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.63 % Allowed : 17.39 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.14), residues: 3419 helix: -0.03 (0.20), residues: 623 sheet: -1.00 (0.22), residues: 586 loop : -1.37 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.019 0.001 TYR B 170 PHE 0.033 0.002 PHE C1103 TRP 0.021 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00406 (28051) covalent geometry : angle 0.66805 (38171) SS BOND : bond 0.00362 ( 36) SS BOND : angle 1.15450 ( 72) hydrogen bonds : bond 0.04851 ( 766) hydrogen bonds : angle 6.59697 ( 2085) link_BETA1-4 : bond 0.00534 ( 7) link_BETA1-4 : angle 1.32807 ( 21) link_NAG-ASN : bond 0.00520 ( 28) link_NAG-ASN : angle 2.43502 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.39 seconds wall clock time: 77 minutes 21.54 seconds (4641.54 seconds total)