Starting phenix.real_space_refine on Thu Mar 5 18:10:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.map" model { file = "/net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r15_14231/03_2026/7r15_14231.cif" } resolution = 4.1 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= 0.004 sd= 0.062 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 104 5.16 5 C 15377 2.51 5 N 3950 2.21 5 O 4669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24100 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7702 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 51, 'TRANS': 931} Chain breaks: 9 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7988 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 50, 'TRANS': 969} Chain breaks: 8 Chain: "C" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7808 Classifications: {'peptide': 997} Link IDs: {'PTRANS': 51, 'TRANS': 945} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.52, per 1000 atoms: 0.23 Number of scatterers: 24100 At special positions: 0 Unit cell: (139.136, 136.962, 198.921, 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 104 16.00 O 4669 8.00 N 3950 7.00 C 15377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 336 " - pdb=" SG CYS B 361 " 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 343 " " NAG A1311 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C1098 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 331 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 50 sheets defined 23.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.368A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.656A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 removed outlier: 3.718A pdb=" N GLY A 799 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.632A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.536A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.759A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.694A 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 989 through 1033 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.565A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.868A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 4.093A pdb=" N SER B 375 " --> pdb=" O ALA B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.557A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.717A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 780 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.755A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.869A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 948 through 967 removed outlier: 3.884A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.705A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.768A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 5.478A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.499A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.825A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.549A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.930A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.768A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.714A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.947A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.535A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.037A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.195A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.519A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.689A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 removed outlier: 3.776A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 317 removed outlier: 5.789A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.684A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.557A pdb=" N LYS A 424 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.159A pdb=" N ASN A 450 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLN A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.777A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.975A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.227A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.681A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 5.923A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.588A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.356A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.995A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.661A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.023A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.573A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.668A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 660 through 661 removed outlier: 6.390A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.512A pdb=" N PHE B1075 " --> pdb=" O ILE B 712 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.811A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.561A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.509A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.564A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.776A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.730A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.982A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 598 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.834A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.079A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.550A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.550A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.757A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.757A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 6.036A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2223 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: 6.35 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7653 1.34 - 1.46: 5374 1.46 - 1.58: 11482 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24638 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 24633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 32582 1.54 - 3.08: 840 3.08 - 4.62: 79 4.62 - 6.15: 11 6.15 - 7.69: 3 Bond angle restraints: 33515 Sorted by residual: angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.53 110.22 3.31 9.80e-01 1.04e+00 1.14e+01 angle pdb=" OG1 THR C 618 " pdb=" CB THR C 618 " pdb=" CG2 THR C 618 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" C ASN C 196 " pdb=" CA ASN C 196 " pdb=" CB ASN C 196 " ideal model delta sigma weight residual 110.14 114.74 -4.60 1.54e+00 4.22e-01 8.92e+00 ... (remaining 33510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 14329 23.30 - 46.60: 726 46.60 - 69.90: 136 69.90 - 93.20: 37 93.20 - 116.50: 3 Dihedral angle restraints: 15231 sinusoidal: 6504 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -4.36 -81.64 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 158.72 -65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -29.85 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 15228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3519 0.079 - 0.159: 396 0.159 - 0.238: 6 0.238 - 0.318: 0 0.318 - 0.397: 5 Chirality restraints: 3926 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3923 not shown) Planarity restraints: 4324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 196 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASN C 196 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN C 196 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 197 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO C 987 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 295 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.028 5.00e-02 4.00e+02 ... (remaining 4321 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 471 2.66 - 3.22: 23523 3.22 - 3.78: 37316 3.78 - 4.34: 48127 4.34 - 4.90: 77070 Nonbonded interactions: 186507 Sorted by model distance: nonbonded pdb=" O ASP A 294 " pdb=" OG SER A 297 " model vdw 2.099 3.040 nonbonded pdb=" O GLN A 965 " pdb=" OG SER A 968 " model vdw 2.142 3.040 nonbonded pdb=" OG SER A 816 " pdb=" OE1 GLU A 819 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" NZ LYS B 378 " model vdw 2.171 3.120 ... (remaining 186502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 94 or resid 99 through 175 or resid 188 through \ 619 or resid 642 through 826 or resid 854 through 1311)) selection = (chain 'B' and (resid 26 through 67 or resid 79 through 94 or resid 99 through 1 \ 06 or resid 115 through 135 or resid 169 through 175 or resid 188 through 241 or \ resid 264 through 619 or resid 642 through 826 or resid 854 through 939 or resi \ d 944 through 1311)) selection = (chain 'C' and (resid 26 through 106 or resid 115 through 135 or resid 169 throu \ gh 241 or resid 264 through 619 or resid 642 through 826 or resid 854 through 13 \ 11)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.600 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 0.079 24719 Z= 0.193 Angle : 0.606 16.692 33720 Z= 0.298 Chirality : 0.045 0.397 3926 Planarity : 0.004 0.054 4284 Dihedral : 14.184 116.501 9495 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 2942 helix: 1.59 (0.22), residues: 614 sheet: -0.37 (0.22), residues: 562 loop : -1.55 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.012 0.001 TYR C 707 PHE 0.020 0.001 PHE C 329 TRP 0.016 0.001 TRP B 64 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00413 (24638) covalent geometry : angle 0.56683 (33515) SS BOND : bond 0.00209 ( 38) SS BOND : angle 0.99213 ( 76) hydrogen bonds : bond 0.23039 ( 812) hydrogen bonds : angle 8.16876 ( 2223) link_BETA1-4 : bond 0.01487 ( 3) link_BETA1-4 : angle 4.93592 ( 9) link_NAG-ASN : bond 0.00494 ( 40) link_NAG-ASN : angle 3.29997 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8239 (t0) cc_final: 0.7956 (t0) REVERT: A 200 TYR cc_start: 0.8078 (m-80) cc_final: 0.7797 (m-80) REVERT: A 392 PHE cc_start: 0.8303 (m-10) cc_final: 0.8097 (m-10) REVERT: A 740 MET cc_start: 0.8054 (tmm) cc_final: 0.7717 (tmm) REVERT: A 901 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 216 LEU cc_start: 0.7984 (mm) cc_final: 0.7695 (tt) REVERT: B 429 PHE cc_start: 0.9142 (t80) cc_final: 0.8428 (t80) REVERT: B 1050 MET cc_start: 0.8625 (ptt) cc_final: 0.8376 (ptt) REVERT: B 1142 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8936 (tm-30) REVERT: C 118 LEU cc_start: 0.8479 (mp) cc_final: 0.8272 (mp) REVERT: C 275 PHE cc_start: 0.8133 (m-80) cc_final: 0.7205 (m-80) REVERT: C 342 PHE cc_start: 0.9348 (m-80) cc_final: 0.9016 (m-80) REVERT: C 369 TYR cc_start: 0.9166 (t80) cc_final: 0.8933 (t80) REVERT: C 456 PHE cc_start: 0.8927 (m-10) cc_final: 0.8515 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1414 time to fit residues: 42.5650 Evaluate side-chains 106 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 556 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 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 = 0.3467 r_free = 0.3467 target = 0.082637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.055189 restraints weight = 92055.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057207 restraints weight = 53986.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057893 restraints weight = 31508.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058386 restraints weight = 26111.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058454 restraints weight = 22726.749| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24719 Z= 0.227 Angle : 0.643 14.481 33720 Z= 0.328 Chirality : 0.046 0.439 3926 Planarity : 0.004 0.053 4284 Dihedral : 7.624 89.572 4109 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2942 helix: 1.39 (0.21), residues: 639 sheet: -0.58 (0.22), residues: 565 loop : -1.61 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.017 0.001 TYR B1067 PHE 0.022 0.002 PHE C 329 TRP 0.009 0.001 TRP B 64 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00508 (24638) covalent geometry : angle 0.61479 (33515) SS BOND : bond 0.00303 ( 38) SS BOND : angle 1.05816 ( 76) hydrogen bonds : bond 0.05668 ( 812) hydrogen bonds : angle 6.39471 ( 2223) link_BETA1-4 : bond 0.01549 ( 3) link_BETA1-4 : angle 4.21165 ( 9) link_NAG-ASN : bond 0.00474 ( 40) link_NAG-ASN : angle 2.93625 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8165 (t0) cc_final: 0.7897 (t0) REVERT: A 559 PHE cc_start: 0.7559 (m-10) cc_final: 0.7301 (m-10) REVERT: A 740 MET cc_start: 0.8462 (tmm) cc_final: 0.8163 (tmm) REVERT: B 64 TRP cc_start: 0.8671 (t60) cc_final: 0.8459 (t60) REVERT: B 201 PHE cc_start: 0.9045 (t80) cc_final: 0.8615 (t80) REVERT: B 216 LEU cc_start: 0.8112 (mm) cc_final: 0.7765 (tt) REVERT: B 298 GLU cc_start: 0.9084 (pt0) cc_final: 0.8858 (pt0) REVERT: B 429 PHE cc_start: 0.9193 (t80) cc_final: 0.8457 (t80) REVERT: B 740 MET cc_start: 0.8691 (ttm) cc_final: 0.7974 (ttm) REVERT: B 1142 GLN cc_start: 0.9256 (tp-100) cc_final: 0.9044 (tm-30) REVERT: C 342 PHE cc_start: 0.9353 (m-80) cc_final: 0.8996 (m-80) REVERT: C 369 TYR cc_start: 0.9233 (t80) cc_final: 0.8977 (t80) REVERT: C 456 PHE cc_start: 0.8970 (m-10) cc_final: 0.8643 (m-10) REVERT: C 1029 MET cc_start: 0.9245 (tpp) cc_final: 0.8829 (tpp) outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.1352 time to fit residues: 38.6461 Evaluate side-chains 109 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 76 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 265 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 606 ASN A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C1010 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056909 restraints weight = 91105.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059568 restraints weight = 53293.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060271 restraints weight = 29593.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060760 restraints weight = 23281.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060911 restraints weight = 20882.759| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24719 Z= 0.137 Angle : 0.572 13.774 33720 Z= 0.286 Chirality : 0.045 0.436 3926 Planarity : 0.004 0.053 4284 Dihedral : 6.874 78.777 4109 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 2942 helix: 1.50 (0.21), residues: 636 sheet: -0.53 (0.21), residues: 566 loop : -1.54 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.016 0.001 TYR B1067 PHE 0.019 0.001 PHE C 329 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00310 (24638) covalent geometry : angle 0.54070 (33515) SS BOND : bond 0.00263 ( 38) SS BOND : angle 1.03500 ( 76) hydrogen bonds : bond 0.04806 ( 812) hydrogen bonds : angle 5.74890 ( 2223) link_BETA1-4 : bond 0.01638 ( 3) link_BETA1-4 : angle 4.22931 ( 9) link_NAG-ASN : bond 0.00462 ( 40) link_NAG-ASN : angle 2.85024 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8181 (t0) cc_final: 0.7870 (t0) REVERT: A 429 PHE cc_start: 0.7316 (t80) cc_final: 0.7086 (t80) REVERT: A 740 MET cc_start: 0.8445 (tmm) cc_final: 0.8132 (tmm) REVERT: B 117 LEU cc_start: 0.9025 (tp) cc_final: 0.8686 (tp) REVERT: B 201 PHE cc_start: 0.8777 (t80) cc_final: 0.8516 (t80) REVERT: B 216 LEU cc_start: 0.7992 (mm) cc_final: 0.7732 (tt) REVERT: B 298 GLU cc_start: 0.9031 (pt0) cc_final: 0.8819 (pt0) REVERT: B 429 PHE cc_start: 0.9194 (t80) cc_final: 0.8535 (t80) REVERT: B 586 ASP cc_start: 0.9094 (t0) cc_final: 0.8454 (m-30) REVERT: B 900 MET cc_start: 0.9107 (pmm) cc_final: 0.8903 (pmm) REVERT: B 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8671 (tpp) REVERT: B 1142 GLN cc_start: 0.9243 (tp-100) cc_final: 0.9025 (tm-30) REVERT: C 342 PHE cc_start: 0.9342 (m-80) cc_final: 0.8950 (m-80) REVERT: C 369 TYR cc_start: 0.9166 (t80) cc_final: 0.8899 (t80) REVERT: C 456 PHE cc_start: 0.8949 (m-10) cc_final: 0.8643 (m-10) REVERT: C 1019 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8361 (tmm-80) REVERT: C 1029 MET cc_start: 0.9374 (tpp) cc_final: 0.8894 (tpp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1372 time to fit residues: 42.6014 Evaluate side-chains 118 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 283 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 159 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056863 restraints weight = 90487.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058724 restraints weight = 50742.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059969 restraints weight = 34441.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060813 restraints weight = 26471.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061383 restraints weight = 22162.377| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24719 Z= 0.112 Angle : 0.550 12.884 33720 Z= 0.273 Chirality : 0.044 0.429 3926 Planarity : 0.004 0.056 4284 Dihedral : 6.212 58.867 4109 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 2942 helix: 1.54 (0.22), residues: 636 sheet: -0.45 (0.21), residues: 576 loop : -1.46 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.016 0.001 TYR B 369 PHE 0.020 0.001 PHE B 135 TRP 0.027 0.001 TRP B 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00251 (24638) covalent geometry : angle 0.51975 (33515) SS BOND : bond 0.00183 ( 38) SS BOND : angle 0.99126 ( 76) hydrogen bonds : bond 0.04346 ( 812) hydrogen bonds : angle 5.46188 ( 2223) link_BETA1-4 : bond 0.01570 ( 3) link_BETA1-4 : angle 4.19819 ( 9) link_NAG-ASN : bond 0.00451 ( 40) link_NAG-ASN : angle 2.75190 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8060 (t0) cc_final: 0.7787 (t0) REVERT: A 1050 MET cc_start: 0.8177 (tmm) cc_final: 0.7874 (tmm) REVERT: B 117 LEU cc_start: 0.8836 (tp) cc_final: 0.8537 (tp) REVERT: B 201 PHE cc_start: 0.8755 (t80) cc_final: 0.8523 (t80) REVERT: B 216 LEU cc_start: 0.8087 (mm) cc_final: 0.7847 (tt) REVERT: B 298 GLU cc_start: 0.9009 (pt0) cc_final: 0.8796 (pt0) REVERT: B 429 PHE cc_start: 0.9226 (t80) cc_final: 0.8678 (t80) REVERT: B 740 MET cc_start: 0.8878 (ttm) cc_final: 0.8412 (ttm) REVERT: B 983 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.8314 (tmm-80) REVERT: B 1029 MET cc_start: 0.9203 (tpp) cc_final: 0.8588 (tpp) REVERT: B 1050 MET cc_start: 0.8862 (ptt) cc_final: 0.8504 (ptt) REVERT: C 275 PHE cc_start: 0.8441 (m-10) cc_final: 0.7789 (m-80) REVERT: C 342 PHE cc_start: 0.9244 (m-80) cc_final: 0.8857 (m-80) REVERT: C 369 TYR cc_start: 0.9016 (t80) cc_final: 0.8782 (t80) REVERT: C 456 PHE cc_start: 0.8899 (m-10) cc_final: 0.8649 (m-10) REVERT: C 1014 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7436 (tpp80) REVERT: C 1019 ARG cc_start: 0.8601 (tmm-80) cc_final: 0.8343 (tmm-80) REVERT: C 1029 MET cc_start: 0.9358 (tpp) cc_final: 0.8913 (tpp) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1382 time to fit residues: 43.6862 Evaluate side-chains 130 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 101 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1036 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1083 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 = 0.3505 r_free = 0.3505 target = 0.084402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056184 restraints weight = 90516.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057999 restraints weight = 51015.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059237 restraints weight = 34780.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060049 restraints weight = 26744.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060557 restraints weight = 22452.707| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24719 Z= 0.162 Angle : 0.572 12.528 33720 Z= 0.285 Chirality : 0.045 0.425 3926 Planarity : 0.004 0.058 4284 Dihedral : 5.876 57.217 4109 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.04 % Allowed : 2.82 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 2942 helix: 1.47 (0.21), residues: 645 sheet: -0.46 (0.21), residues: 581 loop : -1.50 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.015 0.001 TYR C1067 PHE 0.022 0.001 PHE C 486 TRP 0.012 0.001 TRP B 64 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00370 (24638) covalent geometry : angle 0.54245 (33515) SS BOND : bond 0.00237 ( 38) SS BOND : angle 1.04290 ( 76) hydrogen bonds : bond 0.04471 ( 812) hydrogen bonds : angle 5.42051 ( 2223) link_BETA1-4 : bond 0.01544 ( 3) link_BETA1-4 : angle 4.19677 ( 9) link_NAG-ASN : bond 0.00404 ( 40) link_NAG-ASN : angle 2.76322 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8113 (t0) cc_final: 0.7786 (t0) REVERT: A 1050 MET cc_start: 0.8360 (tmm) cc_final: 0.7965 (tmm) REVERT: B 117 LEU cc_start: 0.8911 (tp) cc_final: 0.8636 (tp) REVERT: B 201 PHE cc_start: 0.8799 (t80) cc_final: 0.8559 (t80) REVERT: B 298 GLU cc_start: 0.9012 (pt0) cc_final: 0.8745 (pt0) REVERT: B 380 TYR cc_start: 0.8961 (t80) cc_final: 0.8735 (t80) REVERT: B 740 MET cc_start: 0.8840 (ttm) cc_final: 0.8472 (ttm) REVERT: B 965 GLN cc_start: 0.8975 (tp40) cc_final: 0.8716 (tp-100) REVERT: B 983 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.8484 (tmm-80) REVERT: B 1050 MET cc_start: 0.8934 (ptt) cc_final: 0.8451 (ptt) REVERT: C 173 GLN cc_start: 0.9197 (mp10) cc_final: 0.8994 (pm20) REVERT: C 342 PHE cc_start: 0.9266 (m-80) cc_final: 0.8872 (m-80) REVERT: C 369 TYR cc_start: 0.8988 (t80) cc_final: 0.8739 (t80) REVERT: C 456 PHE cc_start: 0.8940 (m-10) cc_final: 0.8688 (m-10) REVERT: C 1014 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7879 (tpp80) REVERT: C 1029 MET cc_start: 0.9397 (tpp) cc_final: 0.8922 (tpp) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1395 time to fit residues: 40.2016 Evaluate side-chains 122 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 203 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 157 optimal weight: 0.0170 chunk 262 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054987 restraints weight = 91341.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057657 restraints weight = 54022.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058196 restraints weight = 30616.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058913 restraints weight = 24335.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.059000 restraints weight = 21419.700| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24719 Z= 0.218 Angle : 0.619 11.976 33720 Z= 0.313 Chirality : 0.045 0.422 3926 Planarity : 0.004 0.054 4284 Dihedral : 5.850 53.598 4109 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.04 % Allowed : 2.17 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2942 helix: 1.32 (0.21), residues: 637 sheet: -0.49 (0.22), residues: 565 loop : -1.57 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.015 0.001 TYR C1067 PHE 0.020 0.002 PHE C 329 TRP 0.009 0.001 TRP B 64 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00495 (24638) covalent geometry : angle 0.59283 (33515) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.12070 ( 76) hydrogen bonds : bond 0.04808 ( 812) hydrogen bonds : angle 5.54130 ( 2223) link_BETA1-4 : bond 0.01533 ( 3) link_BETA1-4 : angle 4.22558 ( 9) link_NAG-ASN : bond 0.00385 ( 40) link_NAG-ASN : angle 2.74664 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8256 (t0) cc_final: 0.7902 (t0) REVERT: A 1050 MET cc_start: 0.8429 (tmm) cc_final: 0.8168 (tmm) REVERT: B 117 LEU cc_start: 0.8999 (tp) cc_final: 0.8221 (tp) REVERT: B 201 PHE cc_start: 0.8861 (t80) cc_final: 0.8497 (t80) REVERT: B 740 MET cc_start: 0.8774 (ttm) cc_final: 0.8531 (ttt) REVERT: B 965 GLN cc_start: 0.9066 (tp40) cc_final: 0.8865 (tp-100) REVERT: B 1050 MET cc_start: 0.8838 (ptt) cc_final: 0.8389 (ptt) REVERT: C 173 GLN cc_start: 0.9315 (mp10) cc_final: 0.9071 (pm20) REVERT: C 342 PHE cc_start: 0.9332 (m-80) cc_final: 0.8926 (m-80) REVERT: C 369 TYR cc_start: 0.9138 (t80) cc_final: 0.8859 (t80) REVERT: C 456 PHE cc_start: 0.9031 (m-10) cc_final: 0.8777 (m-10) REVERT: C 1014 ARG cc_start: 0.8294 (ttm110) cc_final: 0.7897 (tpp80) REVERT: C 1029 MET cc_start: 0.9389 (tpp) cc_final: 0.8938 (tpp) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1362 time to fit residues: 38.0865 Evaluate side-chains 113 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 159 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055663 restraints weight = 91803.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057473 restraints weight = 52117.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058689 restraints weight = 35524.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059507 restraints weight = 27547.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059943 restraints weight = 23161.871| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24719 Z= 0.158 Angle : 0.580 11.655 33720 Z= 0.291 Chirality : 0.045 0.412 3926 Planarity : 0.004 0.052 4284 Dihedral : 5.770 59.951 4109 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 2942 helix: 1.43 (0.21), residues: 636 sheet: -0.42 (0.22), residues: 562 loop : -1.57 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.015 0.001 TYR B 369 PHE 0.021 0.001 PHE C 329 TRP 0.008 0.001 TRP B 64 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00358 (24638) covalent geometry : angle 0.54888 (33515) SS BOND : bond 0.00203 ( 38) SS BOND : angle 1.01616 ( 76) hydrogen bonds : bond 0.04545 ( 812) hydrogen bonds : angle 5.34652 ( 2223) link_BETA1-4 : bond 0.01577 ( 3) link_BETA1-4 : angle 4.15317 ( 9) link_NAG-ASN : bond 0.00390 ( 40) link_NAG-ASN : angle 2.93034 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8168 (t0) cc_final: 0.7799 (t0) REVERT: A 1050 MET cc_start: 0.8425 (tmm) cc_final: 0.8144 (tmm) REVERT: B 117 LEU cc_start: 0.8849 (tp) cc_final: 0.8589 (tp) REVERT: B 380 TYR cc_start: 0.8962 (t80) cc_final: 0.8734 (t80) REVERT: B 697 MET cc_start: 0.8423 (ptp) cc_final: 0.7714 (ptp) REVERT: B 740 MET cc_start: 0.8861 (ttm) cc_final: 0.8621 (tpp) REVERT: B 965 GLN cc_start: 0.9018 (tp40) cc_final: 0.8805 (tp-100) REVERT: B 1050 MET cc_start: 0.8886 (ptt) cc_final: 0.8505 (ptt) REVERT: C 275 PHE cc_start: 0.8508 (m-10) cc_final: 0.7997 (m-80) REVERT: C 342 PHE cc_start: 0.9291 (m-80) cc_final: 0.8875 (m-80) REVERT: C 369 TYR cc_start: 0.9010 (t80) cc_final: 0.8764 (t80) REVERT: C 456 PHE cc_start: 0.8985 (m-10) cc_final: 0.8737 (m-10) REVERT: C 1014 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7841 (tpp80) REVERT: C 1019 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8444 (tmm-80) REVERT: C 1029 MET cc_start: 0.9437 (tpp) cc_final: 0.8948 (tpp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1386 time to fit residues: 39.8379 Evaluate side-chains 116 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 209 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 268 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.084943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056422 restraints weight = 91297.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058254 restraints weight = 51529.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059465 restraints weight = 35204.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060322 restraints weight = 27180.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060853 restraints weight = 22792.060| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24719 Z= 0.115 Angle : 0.555 11.184 33720 Z= 0.277 Chirality : 0.045 0.398 3926 Planarity : 0.004 0.055 4284 Dihedral : 5.508 59.372 4109 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.04 % Allowed : 1.03 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2942 helix: 1.56 (0.22), residues: 634 sheet: -0.38 (0.22), residues: 570 loop : -1.48 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.015 0.001 TYR B 369 PHE 0.020 0.001 PHE C 329 TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00263 (24638) covalent geometry : angle 0.52524 (33515) SS BOND : bond 0.00195 ( 38) SS BOND : angle 1.06436 ( 76) hydrogen bonds : bond 0.04206 ( 812) hydrogen bonds : angle 5.14658 ( 2223) link_BETA1-4 : bond 0.01525 ( 3) link_BETA1-4 : angle 4.17482 ( 9) link_NAG-ASN : bond 0.00447 ( 40) link_NAG-ASN : angle 2.71905 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8145 (t0) cc_final: 0.7761 (t0) REVERT: A 392 PHE cc_start: 0.8381 (m-10) cc_final: 0.8058 (m-10) REVERT: A 1050 MET cc_start: 0.8529 (tmm) cc_final: 0.8258 (tmm) REVERT: B 117 LEU cc_start: 0.8893 (tp) cc_final: 0.8045 (tp) REVERT: B 201 PHE cc_start: 0.8812 (t80) cc_final: 0.8538 (t80) REVERT: B 298 GLU cc_start: 0.9088 (pt0) cc_final: 0.8849 (pt0) REVERT: B 380 TYR cc_start: 0.8986 (t80) cc_final: 0.8753 (t80) REVERT: B 965 GLN cc_start: 0.8887 (tp40) cc_final: 0.8631 (tp-100) REVERT: B 1050 MET cc_start: 0.8868 (ptt) cc_final: 0.8528 (ptt) REVERT: C 275 PHE cc_start: 0.8398 (m-10) cc_final: 0.7901 (m-80) REVERT: C 342 PHE cc_start: 0.9274 (m-80) cc_final: 0.8876 (m-80) REVERT: C 369 TYR cc_start: 0.8973 (t80) cc_final: 0.8734 (t80) REVERT: C 456 PHE cc_start: 0.8982 (m-10) cc_final: 0.8603 (m-80) REVERT: C 1014 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7758 (tpp80) REVERT: C 1019 ARG cc_start: 0.8630 (tmm-80) cc_final: 0.8363 (tmm-80) REVERT: C 1029 MET cc_start: 0.9421 (tpp) cc_final: 0.8890 (tpp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1295 time to fit residues: 38.9099 Evaluate side-chains 130 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 206 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 226 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.085378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057585 restraints weight = 91434.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060168 restraints weight = 54117.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060876 restraints weight = 30062.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061324 restraints weight = 24231.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061499 restraints weight = 21486.273| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24719 Z= 0.117 Angle : 0.555 11.028 33720 Z= 0.278 Chirality : 0.044 0.395 3926 Planarity : 0.004 0.055 4284 Dihedral : 5.397 58.633 4109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2942 helix: 1.55 (0.22), residues: 639 sheet: -0.32 (0.22), residues: 558 loop : -1.46 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1014 TYR 0.015 0.001 TYR B 369 PHE 0.020 0.001 PHE C 329 TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00268 (24638) covalent geometry : angle 0.52561 (33515) SS BOND : bond 0.00169 ( 38) SS BOND : angle 1.25198 ( 76) hydrogen bonds : bond 0.04142 ( 812) hydrogen bonds : angle 5.09510 ( 2223) link_BETA1-4 : bond 0.01527 ( 3) link_BETA1-4 : angle 4.14649 ( 9) link_NAG-ASN : bond 0.00420 ( 40) link_NAG-ASN : angle 2.64949 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8200 (t0) cc_final: 0.7822 (t0) REVERT: A 198 ASP cc_start: 0.8811 (m-30) cc_final: 0.8450 (m-30) REVERT: A 1050 MET cc_start: 0.8593 (tmm) cc_final: 0.8123 (tmm) REVERT: B 117 LEU cc_start: 0.9030 (tp) cc_final: 0.8753 (tp) REVERT: B 298 GLU cc_start: 0.9087 (pt0) cc_final: 0.8847 (pt0) REVERT: B 740 MET cc_start: 0.8757 (ttt) cc_final: 0.7798 (ttt) REVERT: B 1050 MET cc_start: 0.8916 (ptt) cc_final: 0.8543 (ptt) REVERT: C 275 PHE cc_start: 0.8344 (m-10) cc_final: 0.7879 (m-80) REVERT: C 342 PHE cc_start: 0.9339 (m-80) cc_final: 0.8943 (m-80) REVERT: C 369 TYR cc_start: 0.9112 (t80) cc_final: 0.8849 (t80) REVERT: C 456 PHE cc_start: 0.9011 (m-10) cc_final: 0.8604 (m-80) REVERT: C 1019 ARG cc_start: 0.8645 (tmm-80) cc_final: 0.8372 (tmm-80) REVERT: C 1029 MET cc_start: 0.9454 (tpp) cc_final: 0.8923 (tpp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1386 time to fit residues: 41.1746 Evaluate side-chains 128 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 154 optimal weight: 0.1980 chunk 138 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** C1083 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 = 0.3525 r_free = 0.3525 target = 0.085521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057653 restraints weight = 91331.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060287 restraints weight = 54348.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.061039 restraints weight = 31452.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061483 restraints weight = 23638.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061675 restraints weight = 21319.410| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24719 Z= 0.108 Angle : 0.549 10.751 33720 Z= 0.275 Chirality : 0.044 0.388 3926 Planarity : 0.004 0.072 4284 Dihedral : 5.238 57.470 4109 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2942 helix: 1.57 (0.22), residues: 634 sheet: -0.18 (0.23), residues: 539 loop : -1.41 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C1014 TYR 0.015 0.001 TYR B 369 PHE 0.021 0.001 PHE B 318 TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00246 (24638) covalent geometry : angle 0.52163 (33515) SS BOND : bond 0.00171 ( 38) SS BOND : angle 1.12083 ( 76) hydrogen bonds : bond 0.04048 ( 812) hydrogen bonds : angle 5.01918 ( 2223) link_BETA1-4 : bond 0.01526 ( 3) link_BETA1-4 : angle 4.14727 ( 9) link_NAG-ASN : bond 0.00422 ( 40) link_NAG-ASN : angle 2.56893 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8178 (t0) cc_final: 0.7842 (t0) REVERT: A 1050 MET cc_start: 0.8566 (tmm) cc_final: 0.8089 (tmm) REVERT: B 117 LEU cc_start: 0.9031 (tp) cc_final: 0.8734 (tp) REVERT: B 298 GLU cc_start: 0.9039 (pt0) cc_final: 0.8829 (pt0) REVERT: B 546 LEU cc_start: 0.7861 (mt) cc_final: 0.7039 (mp) REVERT: B 740 MET cc_start: 0.8776 (ttt) cc_final: 0.8377 (ttt) REVERT: B 1029 MET cc_start: 0.9073 (tpp) cc_final: 0.8819 (tpp) REVERT: B 1050 MET cc_start: 0.8885 (ptt) cc_final: 0.8494 (ptt) REVERT: C 342 PHE cc_start: 0.9324 (m-80) cc_final: 0.8941 (m-80) REVERT: C 369 TYR cc_start: 0.9040 (t80) cc_final: 0.8811 (t80) REVERT: C 456 PHE cc_start: 0.8998 (m-10) cc_final: 0.8601 (m-80) REVERT: C 1019 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8369 (tmm-80) REVERT: C 1029 MET cc_start: 0.9431 (tpp) cc_final: 0.8894 (tpp) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1343 time to fit residues: 41.4462 Evaluate side-chains 127 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 181 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 289 optimal weight: 0.1980 chunk 163 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 117 optimal weight: 0.0570 chunk 118 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 360 ASN A 907 ASN B 954 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1083 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 = 0.3537 r_free = 0.3537 target = 0.086106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058404 restraints weight = 91378.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060950 restraints weight = 53730.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061656 restraints weight = 30560.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062161 restraints weight = 24306.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062375 restraints weight = 21360.666| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24719 Z= 0.097 Angle : 0.536 10.540 33720 Z= 0.269 Chirality : 0.044 0.381 3926 Planarity : 0.004 0.057 4284 Dihedral : 5.090 56.448 4109 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.08 % Allowed : 0.19 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2942 helix: 1.66 (0.22), residues: 632 sheet: -0.08 (0.22), residues: 548 loop : -1.38 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1014 TYR 0.017 0.001 TYR C 351 PHE 0.021 0.001 PHE A 92 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00218 (24638) covalent geometry : angle 0.50994 (33515) SS BOND : bond 0.00122 ( 38) SS BOND : angle 1.03713 ( 76) hydrogen bonds : bond 0.03847 ( 812) hydrogen bonds : angle 4.93962 ( 2223) link_BETA1-4 : bond 0.01519 ( 3) link_BETA1-4 : angle 4.10804 ( 9) link_NAG-ASN : bond 0.00431 ( 40) link_NAG-ASN : angle 2.50399 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.90 seconds wall clock time: 59 minutes 31.96 seconds (3571.96 seconds total)