Starting phenix.real_space_refine on Sat Jun 21 03:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r15_14231/06_2025/7r15_14231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r15_14231/06_2025/7r15_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_14231/06_2025/7r15_14231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r15_14231/06_2025/7r15_14231.map" model { file = "/net/cci-nas-00/data/ceres_data/7r15_14231/06_2025/7r15_14231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r15_14231/06_2025/7r15_14231.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.26, per 1000 atoms: 0.63 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: 6.31 Conformation dependent library (CDL) restraints added in 3.1 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: 4.16 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: 10.64 Time building geometry restraints manager: 7.48 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 1146 or resid 1301 through 13 \ 11)) 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 1146 or resid 1301 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 11 \ 46 or resid 1301 through 1311)) } 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.980 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (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 TRP 0.016 0.001 TRP B 64 HIS 0.006 0.001 HIS C 49 PHE 0.020 0.001 PHE C 329 TYR 0.012 0.001 TYR C 707 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 40) link_NAG-ASN : angle 3.29997 ( 120) link_BETA1-4 : bond 0.01487 ( 3) link_BETA1-4 : angle 4.93592 ( 9) hydrogen bonds : bond 0.23039 ( 812) hydrogen bonds : angle 8.16876 ( 2223) SS BOND : bond 0.00209 ( 38) SS BOND : angle 0.99213 ( 76) covalent geometry : bond 0.00413 (24638) covalent geometry : angle 0.56683 (33515) *********************** 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 : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8239 (t0) cc_final: 0.7957 (t0) REVERT: A 392 PHE cc_start: 0.8303 (m-10) cc_final: 0.8098 (m-10) REVERT: A 740 MET cc_start: 0.8054 (tmm) cc_final: 0.7718 (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: 0.8427 (t80) REVERT: B 1050 MET cc_start: 0.8625 (ptt) cc_final: 0.8374 (ptt) REVERT: B 1142 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8935 (tm-30) REVERT: C 118 LEU cc_start: 0.8480 (mp) cc_final: 0.8273 (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: 0.8508 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3230 time to fit residues: 96.8808 Evaluate side-chains 108 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 271 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 49 HIS B 439 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055358 restraints weight = 92476.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057180 restraints weight = 53751.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057873 restraints weight = 32364.132| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24719 Z= 0.246 Angle : 0.659 14.200 33720 Z= 0.333 Chirality : 0.046 0.443 3926 Planarity : 0.004 0.053 4284 Dihedral : 7.585 88.849 4109 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.11 % Allowed : 5.83 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 2942 helix: 1.32 (0.21), residues: 640 sheet: -0.68 (0.22), residues: 560 loop : -1.64 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.006 0.001 HIS B1064 PHE 0.023 0.002 PHE C 329 TYR 0.018 0.002 TYR B1067 ARG 0.004 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 40) link_NAG-ASN : angle 2.92543 ( 120) link_BETA1-4 : bond 0.01436 ( 3) link_BETA1-4 : angle 4.23316 ( 9) hydrogen bonds : bond 0.05561 ( 812) hydrogen bonds : angle 6.36422 ( 2223) SS BOND : bond 0.00388 ( 38) SS BOND : angle 1.09917 ( 76) covalent geometry : bond 0.00551 (24638) covalent geometry : angle 0.63110 (33515) *********************** 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 164 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8208 (t0) cc_final: 0.7933 (t0) REVERT: A 429 PHE cc_start: 0.7325 (t80) cc_final: 0.7103 (t80) REVERT: A 740 MET cc_start: 0.8491 (tmm) cc_final: 0.8184 (tmm) REVERT: B 201 PHE cc_start: 0.9050 (t80) cc_final: 0.8644 (t80) REVERT: B 216 LEU cc_start: 0.8256 (mm) cc_final: 0.7908 (tt) REVERT: B 298 GLU cc_start: 0.9109 (pt0) cc_final: 0.8890 (pt0) REVERT: B 429 PHE cc_start: 0.9226 (t80) cc_final: 0.8499 (t80) REVERT: B 740 MET cc_start: 0.8677 (ttm) cc_final: 0.8023 (ttm) REVERT: B 900 MET cc_start: 0.9109 (pmm) cc_final: 0.8904 (pmm) REVERT: B 1050 MET cc_start: 0.8855 (ptt) cc_final: 0.8422 (ptt) REVERT: B 1142 GLN cc_start: 0.9297 (tp-100) cc_final: 0.9078 (tm-30) REVERT: C 342 PHE cc_start: 0.9371 (m-80) cc_final: 0.8997 (m-80) REVERT: C 369 TYR cc_start: 0.9262 (t80) cc_final: 0.8994 (t80) REVERT: C 456 PHE cc_start: 0.8976 (m-10) cc_final: 0.8669 (m-10) REVERT: C 1029 MET cc_start: 0.9281 (tpp) cc_final: 0.8891 (tpp) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.2881 time to fit residues: 81.1752 Evaluate side-chains 107 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 250 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 262 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 39 optimal weight: 0.0980 chunk 215 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 C 388 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3484 r_free = 0.3484 target = 0.083349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.055552 restraints weight = 91293.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058264 restraints weight = 54545.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059004 restraints weight = 30338.952| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24719 Z= 0.195 Angle : 0.613 13.876 33720 Z= 0.308 Chirality : 0.045 0.438 3926 Planarity : 0.004 0.054 4284 Dihedral : 7.105 83.324 4109 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 2942 helix: 1.30 (0.21), residues: 644 sheet: -0.60 (0.21), residues: 570 loop : -1.66 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.020 0.001 PHE C 329 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 40) link_NAG-ASN : angle 2.91357 ( 120) link_BETA1-4 : bond 0.01560 ( 3) link_BETA1-4 : angle 4.23543 ( 9) hydrogen bonds : bond 0.05165 ( 812) hydrogen bonds : angle 5.95815 ( 2223) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.13599 ( 76) covalent geometry : bond 0.00441 (24638) covalent geometry : angle 0.58270 (33515) *********************** 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 164 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8168 (t0) cc_final: 0.7883 (t0) REVERT: A 429 PHE cc_start: 0.7383 (t80) cc_final: 0.7148 (t80) REVERT: A 740 MET cc_start: 0.8448 (tmm) cc_final: 0.8146 (tmm) REVERT: B 117 LEU cc_start: 0.9041 (tp) cc_final: 0.8720 (tp) REVERT: B 201 PHE cc_start: 0.8762 (t80) cc_final: 0.8508 (t80) REVERT: B 216 LEU cc_start: 0.8168 (mm) cc_final: 0.7882 (tt) REVERT: B 298 GLU cc_start: 0.9023 (pt0) cc_final: 0.8822 (pt0) REVERT: B 429 PHE cc_start: 0.9232 (t80) cc_final: 0.8475 (t80) REVERT: B 586 ASP cc_start: 0.9098 (t0) cc_final: 0.8498 (m-30) REVERT: B 1050 MET cc_start: 0.8787 (ptt) cc_final: 0.8357 (ptt) REVERT: B 1142 GLN cc_start: 0.9251 (tp-100) cc_final: 0.9040 (tm-30) REVERT: C 275 PHE cc_start: 0.8546 (m-80) cc_final: 0.7696 (m-80) REVERT: C 342 PHE cc_start: 0.9348 (m-80) cc_final: 0.8954 (m-80) REVERT: C 369 TYR cc_start: 0.9121 (t80) cc_final: 0.8876 (t80) REVERT: C 456 PHE cc_start: 0.8984 (m-10) cc_final: 0.8667 (m-10) REVERT: C 1029 MET cc_start: 0.9433 (tpp) cc_final: 0.8972 (tpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.3055 time to fit residues: 85.0756 Evaluate side-chains 111 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 184 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 295 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** 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 = 0.3508 r_free = 0.3508 target = 0.084578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056894 restraints weight = 91248.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059378 restraints weight = 55158.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.060020 restraints weight = 30959.765| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1440 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= 0.148 Angle : 0.576 12.897 33720 Z= 0.288 Chirality : 0.045 0.434 3926 Planarity : 0.004 0.055 4284 Dihedral : 6.486 62.791 4109 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 2942 helix: 1.36 (0.21), residues: 644 sheet: -0.59 (0.21), residues: 578 loop : -1.58 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.010 0.001 HIS B1083 PHE 0.022 0.001 PHE C 486 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 40) link_NAG-ASN : angle 2.80116 ( 120) link_BETA1-4 : bond 0.01507 ( 3) link_BETA1-4 : angle 4.24340 ( 9) hydrogen bonds : bond 0.04675 ( 812) hydrogen bonds : angle 5.62872 ( 2223) SS BOND : bond 0.00294 ( 38) SS BOND : angle 1.04973 ( 76) covalent geometry : bond 0.00337 (24638) covalent geometry : angle 0.54586 (33515) *********************** 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 175 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8206 (t0) cc_final: 0.7908 (t0) REVERT: A 1050 MET cc_start: 0.8166 (tmm) cc_final: 0.7810 (tmm) REVERT: B 117 LEU cc_start: 0.9005 (tp) cc_final: 0.8732 (tp) REVERT: B 201 PHE cc_start: 0.8754 (t80) cc_final: 0.8527 (t80) REVERT: B 216 LEU cc_start: 0.8174 (mm) cc_final: 0.7955 (tt) REVERT: B 429 PHE cc_start: 0.9188 (t80) cc_final: 0.8511 (t80) REVERT: B 1029 MET cc_start: 0.9232 (tpp) cc_final: 0.8676 (tpp) REVERT: B 1050 MET cc_start: 0.8780 (ptt) cc_final: 0.8380 (ptt) REVERT: C 342 PHE cc_start: 0.9338 (m-80) cc_final: 0.8949 (m-80) REVERT: C 369 TYR cc_start: 0.9145 (t80) cc_final: 0.8919 (t80) REVERT: C 456 PHE cc_start: 0.8960 (m-10) cc_final: 0.8657 (m-10) REVERT: C 1019 ARG cc_start: 0.8643 (tmm-80) cc_final: 0.8398 (tmm-80) REVERT: C 1029 MET cc_start: 0.9425 (tpp) cc_final: 0.8970 (tpp) outliers start: 2 outliers final: 0 residues processed: 174 average time/residue: 0.3189 time to fit residues: 93.3015 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 : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 155 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 292 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.084102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055841 restraints weight = 91773.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058554 restraints weight = 54374.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059161 restraints weight = 31246.267| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24719 Z= 0.153 Angle : 0.576 12.415 33720 Z= 0.287 Chirality : 0.045 0.423 3926 Planarity : 0.004 0.053 4284 Dihedral : 6.011 55.539 4109 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 2942 helix: 1.46 (0.21), residues: 639 sheet: -0.55 (0.21), residues: 581 loop : -1.58 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.007 0.001 HIS B1083 PHE 0.020 0.001 PHE C 329 TYR 0.015 0.001 TYR B 369 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 40) link_NAG-ASN : angle 2.77962 ( 120) link_BETA1-4 : bond 0.01534 ( 3) link_BETA1-4 : angle 4.23409 ( 9) hydrogen bonds : bond 0.04548 ( 812) hydrogen bonds : angle 5.47261 ( 2223) SS BOND : bond 0.00236 ( 38) SS BOND : angle 1.09567 ( 76) covalent geometry : bond 0.00349 (24638) covalent geometry : angle 0.54639 (33515) *********************** 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 171 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9012 (t80) cc_final: 0.8768 (t80) REVERT: A 99 ASN cc_start: 0.8264 (t0) cc_final: 0.7906 (t0) REVERT: A 1050 MET cc_start: 0.8365 (tmm) cc_final: 0.7915 (tmm) REVERT: B 117 LEU cc_start: 0.8988 (tp) cc_final: 0.8241 (tp) REVERT: B 201 PHE cc_start: 0.8796 (t80) cc_final: 0.8405 (t80) REVERT: B 298 GLU cc_start: 0.9057 (pt0) cc_final: 0.8850 (pt0) REVERT: B 740 MET cc_start: 0.8929 (ttm) cc_final: 0.8659 (ttm) REVERT: B 1050 MET cc_start: 0.8776 (ptt) cc_final: 0.8415 (ptt) REVERT: C 342 PHE cc_start: 0.9342 (m-80) cc_final: 0.8933 (m-80) REVERT: C 369 TYR cc_start: 0.9133 (t80) cc_final: 0.8881 (t80) REVERT: C 456 PHE cc_start: 0.8976 (m-10) cc_final: 0.8685 (m-10) REVERT: C 1014 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7621 (tpp80) REVERT: C 1019 ARG cc_start: 0.8691 (tmm-80) cc_final: 0.8439 (tmm-80) REVERT: C 1029 MET cc_start: 0.9420 (tpp) cc_final: 0.8915 (tpp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3107 time to fit residues: 89.1028 Evaluate side-chains 120 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 167 optimal weight: 0.0870 chunk 236 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 278 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.085477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.057917 restraints weight = 90116.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060534 restraints weight = 54902.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061029 restraints weight = 31139.084| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1733 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= 0.113 Angle : 0.556 11.942 33720 Z= 0.278 Chirality : 0.045 0.412 3926 Planarity : 0.004 0.052 4284 Dihedral : 5.768 59.772 4109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 2942 helix: 1.49 (0.21), residues: 645 sheet: -0.48 (0.21), residues: 578 loop : -1.55 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS B1083 PHE 0.020 0.001 PHE C 329 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 40) link_NAG-ASN : angle 2.84581 ( 120) link_BETA1-4 : bond 0.01526 ( 3) link_BETA1-4 : angle 4.17183 ( 9) hydrogen bonds : bond 0.04322 ( 812) hydrogen bonds : angle 5.31249 ( 2223) SS BOND : bond 0.00252 ( 38) SS BOND : angle 1.07264 ( 76) covalent geometry : bond 0.00256 (24638) covalent geometry : angle 0.52460 (33515) *********************** 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 185 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9005 (t80) cc_final: 0.8757 (t80) REVERT: A 99 ASN cc_start: 0.8257 (t0) cc_final: 0.7903 (t0) REVERT: A 314 GLN cc_start: 0.8393 (tp40) cc_final: 0.8127 (tp40) REVERT: A 1050 MET cc_start: 0.8386 (tmm) cc_final: 0.7893 (tmm) REVERT: B 106 PHE cc_start: 0.8561 (m-10) cc_final: 0.8280 (m-10) REVERT: B 117 LEU cc_start: 0.8999 (tp) cc_final: 0.8554 (tp) REVERT: B 201 PHE cc_start: 0.8774 (t80) cc_final: 0.8546 (t80) REVERT: B 318 PHE cc_start: 0.8427 (t80) cc_final: 0.8217 (t80) REVERT: B 380 TYR cc_start: 0.8895 (t80) cc_final: 0.8694 (t80) REVERT: B 983 ARG cc_start: 0.9244 (tmt-80) cc_final: 0.9019 (tmt-80) REVERT: B 1050 MET cc_start: 0.8775 (ptt) cc_final: 0.8389 (ptt) REVERT: C 173 GLN cc_start: 0.9306 (mp10) cc_final: 0.9070 (pm20) REVERT: C 342 PHE cc_start: 0.9326 (m-80) cc_final: 0.8919 (m-80) REVERT: C 369 TYR cc_start: 0.9060 (t80) cc_final: 0.8817 (t80) REVERT: C 456 PHE cc_start: 0.8955 (m-10) cc_final: 0.8651 (m-10) REVERT: C 1014 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7724 (tpp80) REVERT: C 1019 ARG cc_start: 0.8639 (tmm-80) cc_final: 0.8374 (tmm-80) REVERT: C 1029 MET cc_start: 0.9424 (tpp) cc_final: 0.8946 (tpp) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3668 time to fit residues: 112.7535 Evaluate side-chains 132 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 170 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 272 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.085374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057506 restraints weight = 90772.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060164 restraints weight = 53349.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060823 restraints weight = 29389.953| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1868 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 : 0.540 11.502 33720 Z= 0.269 Chirality : 0.044 0.402 3926 Planarity : 0.004 0.056 4284 Dihedral : 5.439 58.824 4109 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2942 helix: 1.61 (0.22), residues: 639 sheet: -0.41 (0.22), residues: 575 loop : -1.46 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.020 0.001 PHE C 329 TYR 0.015 0.001 TYR B 369 ARG 0.004 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 40) link_NAG-ASN : angle 2.68871 ( 120) link_BETA1-4 : bond 0.01575 ( 3) link_BETA1-4 : angle 4.17611 ( 9) hydrogen bonds : bond 0.04033 ( 812) hydrogen bonds : angle 5.07763 ( 2223) SS BOND : bond 0.00144 ( 38) SS BOND : angle 0.91371 ( 76) covalent geometry : bond 0.00246 (24638) covalent geometry : angle 0.51068 (33515) *********************** 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 195 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8294 (t0) cc_final: 0.7920 (t0) REVERT: A 1050 MET cc_start: 0.8428 (tmm) cc_final: 0.8099 (tmm) REVERT: B 106 PHE cc_start: 0.8586 (m-10) cc_final: 0.8227 (m-10) REVERT: B 117 LEU cc_start: 0.9048 (tp) cc_final: 0.8717 (tp) REVERT: B 201 PHE cc_start: 0.8753 (t80) cc_final: 0.8493 (t80) REVERT: B 298 GLU cc_start: 0.9043 (pt0) cc_final: 0.8839 (pt0) REVERT: B 380 TYR cc_start: 0.8947 (t80) cc_final: 0.8733 (t80) REVERT: B 740 MET cc_start: 0.8926 (ttm) cc_final: 0.8599 (ttm) REVERT: B 965 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8461 (tp-100) REVERT: C 173 GLN cc_start: 0.9332 (mp10) cc_final: 0.9128 (pm20) REVERT: C 342 PHE cc_start: 0.9362 (m-80) cc_final: 0.8937 (m-80) REVERT: C 369 TYR cc_start: 0.9114 (t80) cc_final: 0.8854 (t80) REVERT: C 456 PHE cc_start: 0.9000 (m-10) cc_final: 0.8582 (m-80) REVERT: C 1014 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7812 (tpp80) REVERT: C 1019 ARG cc_start: 0.8625 (tmm-80) cc_final: 0.8336 (tmm-80) REVERT: C 1029 MET cc_start: 0.9461 (tpp) cc_final: 0.8914 (tpp) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3162 time to fit residues: 101.7405 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 : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.085047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057459 restraints weight = 90871.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059961 restraints weight = 52679.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060822 restraints weight = 29590.744| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24719 Z= 0.139 Angle : 0.561 11.229 33720 Z= 0.282 Chirality : 0.044 0.401 3926 Planarity : 0.004 0.079 4284 Dihedral : 5.406 58.589 4109 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2942 helix: 1.54 (0.22), residues: 639 sheet: -0.43 (0.21), residues: 576 loop : -1.45 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.023 0.001 PHE A 92 TYR 0.020 0.001 TYR C 695 ARG 0.016 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 40) link_NAG-ASN : angle 2.62098 ( 120) link_BETA1-4 : bond 0.01570 ( 3) link_BETA1-4 : angle 4.16956 ( 9) hydrogen bonds : bond 0.04164 ( 812) hydrogen bonds : angle 5.14093 ( 2223) SS BOND : bond 0.00248 ( 38) SS BOND : angle 1.03225 ( 76) covalent geometry : bond 0.00317 (24638) covalent geometry : angle 0.53418 (33515) *********************** 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 177 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8245 (t0) cc_final: 0.7888 (t0) REVERT: A 198 ASP cc_start: 0.8834 (m-30) cc_final: 0.8479 (m-30) REVERT: A 1050 MET cc_start: 0.8578 (tmm) cc_final: 0.8267 (tmm) REVERT: B 117 LEU cc_start: 0.9031 (tp) cc_final: 0.8723 (tp) REVERT: B 298 GLU cc_start: 0.9047 (pt0) cc_final: 0.8829 (pt0) REVERT: B 740 MET cc_start: 0.8903 (ttm) cc_final: 0.8467 (ttm) REVERT: B 965 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8585 (tp-100) REVERT: B 1050 MET cc_start: 0.8895 (ptt) cc_final: 0.8542 (ptt) REVERT: C 266 TYR cc_start: 0.7618 (m-80) cc_final: 0.7336 (m-10) REVERT: C 275 PHE cc_start: 0.8366 (m-10) cc_final: 0.7930 (m-80) REVERT: C 342 PHE cc_start: 0.9352 (m-80) cc_final: 0.8949 (m-80) REVERT: C 369 TYR cc_start: 0.9104 (t80) cc_final: 0.8851 (t80) REVERT: C 456 PHE cc_start: 0.9017 (m-10) cc_final: 0.8604 (m-80) REVERT: C 1014 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7814 (tpp80) REVERT: C 1019 ARG cc_start: 0.8699 (tmm-80) cc_final: 0.8410 (tmm-80) REVERT: C 1029 MET cc_start: 0.9460 (tpp) cc_final: 0.8942 (tpp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3034 time to fit residues: 89.7441 Evaluate side-chains 125 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 117 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 291 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.085167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.057098 restraints weight = 91054.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060141 restraints weight = 52456.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060817 restraints weight = 28182.357| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2008 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= 0.126 Angle : 0.562 11.147 33720 Z= 0.280 Chirality : 0.045 0.415 3926 Planarity : 0.004 0.053 4284 Dihedral : 5.361 58.474 4109 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 2942 helix: 1.55 (0.22), residues: 635 sheet: -0.32 (0.22), residues: 571 loop : -1.44 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.022 0.001 PHE A 92 TYR 0.015 0.001 TYR B 369 ARG 0.009 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 40) link_NAG-ASN : angle 2.83817 ( 120) link_BETA1-4 : bond 0.01500 ( 3) link_BETA1-4 : angle 4.16167 ( 9) hydrogen bonds : bond 0.04102 ( 812) hydrogen bonds : angle 5.09624 ( 2223) SS BOND : bond 0.00199 ( 38) SS BOND : angle 1.21900 ( 76) covalent geometry : bond 0.00288 (24638) covalent geometry : angle 0.52951 (33515) *********************** 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 180 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8920 (t80) cc_final: 0.8610 (t80) REVERT: A 99 ASN cc_start: 0.8213 (t0) cc_final: 0.7857 (t0) REVERT: A 1050 MET cc_start: 0.8514 (tmm) cc_final: 0.8194 (tmm) REVERT: B 117 LEU cc_start: 0.8990 (tp) cc_final: 0.8373 (tp) REVERT: B 298 GLU cc_start: 0.9041 (pt0) cc_final: 0.8820 (pt0) REVERT: B 740 MET cc_start: 0.8868 (ttm) cc_final: 0.8473 (ttm) REVERT: B 965 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8583 (tp-100) REVERT: B 1050 MET cc_start: 0.8889 (ptt) cc_final: 0.8529 (ptt) REVERT: C 275 PHE cc_start: 0.8305 (m-10) cc_final: 0.7902 (m-80) REVERT: C 342 PHE cc_start: 0.9338 (m-80) cc_final: 0.8957 (m-80) REVERT: C 369 TYR cc_start: 0.9088 (t80) cc_final: 0.8831 (t80) REVERT: C 456 PHE cc_start: 0.9033 (m-10) cc_final: 0.8624 (m-80) REVERT: C 1019 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8365 (tmm-80) REVERT: C 1029 MET cc_start: 0.9452 (tpp) cc_final: 0.8967 (tpp) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.3120 time to fit residues: 94.2138 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 : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 33 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 254 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 59 optimal weight: 0.1980 chunk 245 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 95 optimal weight: 0.0040 chunk 36 optimal weight: 10.0000 chunk 248 optimal weight: 0.0980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN C1010 GLN C1036 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 = 0.3548 r_free = 0.3548 target = 0.086722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058574 restraints weight = 90617.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060473 restraints weight = 50422.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061741 restraints weight = 34113.716| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2218 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= 0.095 Angle : 0.549 10.662 33720 Z= 0.272 Chirality : 0.045 0.382 3926 Planarity : 0.004 0.056 4284 Dihedral : 5.165 57.879 4109 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2942 helix: 1.63 (0.22), residues: 636 sheet: -0.12 (0.22), residues: 543 loop : -1.34 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.023 0.001 PHE B 318 TYR 0.016 0.001 TYR B 369 ARG 0.006 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 40) link_NAG-ASN : angle 2.61090 ( 120) link_BETA1-4 : bond 0.01580 ( 3) link_BETA1-4 : angle 4.13726 ( 9) hydrogen bonds : bond 0.03762 ( 812) hydrogen bonds : angle 4.92315 ( 2223) SS BOND : bond 0.00171 ( 38) SS BOND : angle 1.13068 ( 76) covalent geometry : bond 0.00209 (24638) covalent geometry : angle 0.52134 (33515) ********************** 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 201 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8953 (t80) cc_final: 0.8704 (t80) REVERT: A 99 ASN cc_start: 0.8161 (t0) cc_final: 0.7796 (t0) REVERT: A 1050 MET cc_start: 0.8559 (tmm) cc_final: 0.8071 (tmm) REVERT: B 117 LEU cc_start: 0.8869 (tp) cc_final: 0.8617 (tp) REVERT: B 298 GLU cc_start: 0.9045 (pt0) cc_final: 0.8837 (pt0) REVERT: B 380 TYR cc_start: 0.8996 (t80) cc_final: 0.8792 (t80) REVERT: B 1050 MET cc_start: 0.8861 (ptt) cc_final: 0.8579 (ptt) REVERT: C 266 TYR cc_start: 0.8112 (m-10) cc_final: 0.7779 (m-10) REVERT: C 342 PHE cc_start: 0.9302 (m-80) cc_final: 0.8924 (m-80) REVERT: C 369 TYR cc_start: 0.8943 (t80) cc_final: 0.8711 (t80) REVERT: C 456 PHE cc_start: 0.8969 (m-10) cc_final: 0.8617 (m-80) REVERT: C 1014 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7716 (tpp80) REVERT: C 1019 ARG cc_start: 0.8598 (tmm-80) cc_final: 0.8310 (tmm-80) REVERT: C 1029 MET cc_start: 0.9433 (tpp) cc_final: 0.8845 (tpp) outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.3531 time to fit residues: 120.4497 Evaluate side-chains 139 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 127 optimal weight: 9.9990 chunk 165 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 286 optimal weight: 0.4980 chunk 148 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056962 restraints weight = 90787.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059526 restraints weight = 54020.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060131 restraints weight = 30063.135| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24719 Z= 0.177 Angle : 0.583 10.430 33720 Z= 0.295 Chirality : 0.045 0.394 3926 Planarity : 0.004 0.052 4284 Dihedral : 5.288 57.964 4109 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2942 helix: 1.49 (0.22), residues: 635 sheet: -0.23 (0.22), residues: 572 loop : -1.40 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1102 HIS 0.005 0.001 HIS A1048 PHE 0.022 0.001 PHE A 92 TYR 0.024 0.001 TYR B 204 ARG 0.010 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 40) link_NAG-ASN : angle 2.60251 ( 120) link_BETA1-4 : bond 0.01487 ( 3) link_BETA1-4 : angle 4.14173 ( 9) hydrogen bonds : bond 0.04230 ( 812) hydrogen bonds : angle 5.13077 ( 2223) SS BOND : bond 0.00273 ( 38) SS BOND : angle 1.14525 ( 76) covalent geometry : bond 0.00402 (24638) covalent geometry : angle 0.55737 (33515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7032.02 seconds wall clock time: 125 minutes 23.86 seconds (7523.86 seconds total)