Starting phenix.real_space_refine on Sun Jul 5 16:58:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4p_28856/07_2026/8f4p_28856.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16951 2.51 5 N 4399 2.21 5 O 5165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26635 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 bond proxies already assigned to first conformer: 8551 Chain: "B" Number of atoms: 8524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 bond proxies already assigned to first conformer: 8708 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} 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 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 459 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.49 residue: pdb=" N ASER B 459 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.33 Time building chain proxies: 7.21, per 1000 atoms: 0.27 Number of scatterers: 26635 At special positions: 0 Unit cell: (163.572, 162.503, 200.991, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5165 8.00 N 4399 7.00 C 16951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 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 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 717 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A1134 " " NAG A1209 " - " ASN A 657 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 717 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 343 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 343 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 47 sheets defined 22.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.824A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.033A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.645A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.840A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.029A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (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 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.702A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.636A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.640A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1032 removed outlier: 4.303A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.742A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.168A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.790A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.652A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.921A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.531A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.603A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.386A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.656A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.827A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.657A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.719A 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 removed outlier: 3.609A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.183A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.151A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.871A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.714A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.737A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.818A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.701A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 removed outlier: 4.379A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.919A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.602A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.667A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.658A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.601A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.774A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 53 removed outlier: 4.301A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 160 through 172 removed outlier: 9.225A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.546A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.560A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.752A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 643 through 645 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.007A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.688A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.474A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.545A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.503A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.594A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.750A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.429A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.833A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.164A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.517A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D 100 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8530 1.34 - 1.47: 6924 1.47 - 1.60: 11647 1.60 - 1.73: 0 1.73 - 1.86: 152 Bond restraints: 27253 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N SER A 884 " pdb=" CA SER A 884 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.67e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.72e+00 bond pdb=" N VAL D 101 " pdb=" CA VAL D 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" N ASP D 100 " pdb=" CA ASP D 100 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 27248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 36549 2.14 - 4.28: 497 4.28 - 6.42: 41 6.42 - 8.56: 8 8.56 - 10.70: 2 Bond angle restraints: 37097 Sorted by residual: angle pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta sigma weight residual 122.65 133.35 -10.70 1.66e+00 3.63e-01 4.15e+01 angle pdb=" CA GLU B 281 " pdb=" CB GLU B 281 " pdb=" CG GLU B 281 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N LEU A 216 " pdb=" CA LEU A 216 " pdb=" C LEU A 216 " ideal model delta sigma weight residual 109.81 116.72 -6.91 2.21e+00 2.05e-01 9.78e+00 angle pdb=" CA ASP D 100 " pdb=" C ASP D 100 " pdb=" O ASP D 100 " ideal model delta sigma weight residual 121.68 118.10 3.58 1.18e+00 7.18e-01 9.19e+00 angle pdb=" N LEU B1141 " pdb=" CA LEU B1141 " pdb=" C LEU B1141 " ideal model delta sigma weight residual 114.62 111.22 3.40 1.14e+00 7.69e-01 8.90e+00 ... (remaining 37092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 14066 18.18 - 36.36: 1445 36.36 - 54.53: 321 54.53 - 72.71: 52 72.71 - 90.89: 22 Dihedral angle restraints: 15906 sinusoidal: 6180 harmonic: 9726 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 18.60 74.40 1 1.00e+01 1.00e-02 7.02e+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 93.00 19.29 73.71 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 22.84 70.16 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 15903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3476 0.054 - 0.108: 686 0.108 - 0.162: 121 0.162 - 0.216: 2 0.216 - 0.270: 4 Chirality restraints: 4289 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG A1207 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1207 " pdb=" O5 NAG A1207 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4286 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 987 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 56 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.24e+00 pdb=" N PRO C 57 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 987 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.032 5.00e-02 4.00e+02 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2121 2.74 - 3.28: 26505 3.28 - 3.82: 42594 3.82 - 4.36: 47430 4.36 - 4.90: 83850 Nonbonded interactions: 202500 Sorted by model distance: nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.197 3.040 nonbonded pdb=" O SER C 975 " pdb=" OG SER C 975 " model vdw 2.198 3.040 nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.220 3.040 nonbonded pdb=" O ALA C 352 " pdb=" OG SER C 399 " model vdw 2.220 3.040 ... (remaining 202495 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 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) selection = (chain 'B' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 617 or resid 641 through 827 or resid 852 through 940 or resid 944 through 11 \ 46 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 0.072 27314 Z= 0.170 Angle : 0.605 10.700 37255 Z= 0.304 Chirality : 0.045 0.270 4289 Planarity : 0.004 0.059 4771 Dihedral : 15.247 90.891 9583 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.51 % Allowed : 23.67 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3314 helix: 1.63 (0.22), residues: 619 sheet: 0.02 (0.22), residues: 587 loop : -1.65 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.015 0.001 PHE C 562 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (27253) covalent geometry : angle 0.59085 / 0.30 (37097) SS BOND : bond 0.00343 / 0.24 ( 25) SS BOND : angle 1.30015 / 1.05 ( 50) hydrogen bonds : bond 0.14375 / 9.34 ( 838) hydrogen bonds : angle 7.21374 / 5.01 ( 2316) link_BETA1-4 : bond 0.00484 / 0.23 ( 6) link_BETA1-4 : angle 2.79098 / 1.60 ( 18) link_NAG-ASN : bond 0.00424 / 0.30 ( 30) link_NAG-ASN : angle 2.27711 / 1.52 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 372 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.7552 (tpt-90) cc_final: 0.7219 (ttt-90) REVERT: C 697 MET cc_start: 0.8407 (mtt) cc_final: 0.8057 (mtp) REVERT: C 808 ASP cc_start: 0.8424 (t0) cc_final: 0.8204 (t0) outliers start: 14 outliers final: 6 residues processed: 383 average time/residue: 0.1459 time to fit residues: 92.6681 Evaluate side-chains 363 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 357 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 703 ASN C 804 GLN C 856 ASN C 907 ASN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.241050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.163230 restraints weight = 66765.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.160765 restraints weight = 28788.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.164463 restraints weight = 19450.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.166141 restraints weight = 13607.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166794 restraints weight = 11588.991| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27314 Z= 0.172 Angle : 0.600 10.120 37255 Z= 0.300 Chirality : 0.046 0.335 4289 Planarity : 0.004 0.057 4771 Dihedral : 4.290 56.375 3600 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 3.19 % Allowed : 21.41 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3314 helix: 1.94 (0.21), residues: 616 sheet: -0.06 (0.21), residues: 624 loop : -1.67 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE C 562 TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (27253) covalent geometry : angle 0.58666 / 0.30 (37097) SS BOND : bond 0.00354 / 0.22 ( 25) SS BOND : angle 1.43169 / 1.06 ( 50) hydrogen bonds : bond 0.04427 / 2.91 ( 838) hydrogen bonds : angle 5.64943 / 3.94 ( 2316) link_BETA1-4 : bond 0.00438 / 0.20 ( 6) link_BETA1-4 : angle 2.04547 / 1.22 ( 18) link_NAG-ASN : bond 0.00412 / 0.29 ( 30) link_NAG-ASN : angle 2.28366 / 1.50 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 375 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8874 (t80) cc_final: 0.8054 (t80) REVERT: A 731 MET cc_start: 0.9153 (ptt) cc_final: 0.8868 (ptt) REVERT: A 979 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: A 1107 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7088 (mpp-170) REVERT: B 542 ASN cc_start: 0.7537 (t0) cc_final: 0.7336 (t0) REVERT: C 228 ASP cc_start: 0.6243 (m-30) cc_final: 0.5825 (m-30) REVERT: C 275 PHE cc_start: 0.5382 (m-80) cc_final: 0.5168 (m-80) REVERT: C 385 THR cc_start: 0.2440 (OUTLIER) cc_final: 0.2208 (m) REVERT: C 697 MET cc_start: 0.8367 (mtt) cc_final: 0.8034 (mtp) REVERT: C 808 ASP cc_start: 0.8379 (t0) cc_final: 0.8019 (t0) REVERT: C 996 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 1029 MET cc_start: 0.8870 (tpp) cc_final: 0.8015 (ttm) REVERT: C 1125 ASN cc_start: 0.8450 (p0) cc_final: 0.7644 (p0) outliers start: 92 outliers final: 48 residues processed: 433 average time/residue: 0.1604 time to fit residues: 114.6135 Evaluate side-chains 406 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 93 optimal weight: 0.5980 chunk 321 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 856 ASN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.240386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.160743 restraints weight = 77293.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.161305 restraints weight = 30958.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.163516 restraints weight = 18366.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.163819 restraints weight = 13625.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.164573 restraints weight = 11911.590| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27314 Z= 0.170 Angle : 0.593 10.251 37255 Z= 0.294 Chirality : 0.046 0.331 4289 Planarity : 0.004 0.057 4771 Dihedral : 4.316 57.185 3597 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 3.84 % Allowed : 21.14 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3314 helix: 1.95 (0.21), residues: 625 sheet: -0.13 (0.21), residues: 649 loop : -1.67 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.022 0.001 TYR A1067 PHE 0.018 0.001 PHE C 562 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (27253) covalent geometry : angle 0.57656 / 0.29 (37097) SS BOND : bond 0.00370 / 0.22 ( 25) SS BOND : angle 1.45258 / 1.06 ( 50) hydrogen bonds : bond 0.04239 / 2.77 ( 838) hydrogen bonds : angle 5.38461 / 3.78 ( 2316) link_BETA1-4 : bond 0.00454 / 0.22 ( 6) link_BETA1-4 : angle 2.08241 / 1.22 ( 18) link_NAG-ASN : bond 0.00451 / 0.31 ( 30) link_NAG-ASN : angle 2.54290 / 1.67 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 378 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9197 (ptt) cc_final: 0.8958 (ptt) REVERT: A 825 LYS cc_start: 0.8396 (tptp) cc_final: 0.8097 (tptp) REVERT: A 979 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: A 1107 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7111 (mpp-170) REVERT: B 457 ARG cc_start: 0.7952 (tpt-90) cc_final: 0.7713 (tpt-90) REVERT: B 790 LYS cc_start: 0.8845 (mttt) cc_final: 0.8383 (mtpp) REVERT: C 228 ASP cc_start: 0.6466 (m-30) cc_final: 0.6085 (m-30) REVERT: C 298 GLU cc_start: 0.7307 (tt0) cc_final: 0.7038 (tt0) REVERT: C 353 TRP cc_start: -0.1213 (OUTLIER) cc_final: -0.1908 (m-90) REVERT: C 385 THR cc_start: 0.2527 (OUTLIER) cc_final: 0.2301 (m) REVERT: C 697 MET cc_start: 0.8360 (mtt) cc_final: 0.7992 (mtp) REVERT: C 808 ASP cc_start: 0.8433 (t0) cc_final: 0.8035 (t0) REVERT: C 811 LYS cc_start: 0.8783 (tppt) cc_final: 0.7947 (tptp) REVERT: C 996 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 1029 MET cc_start: 0.8790 (tpp) cc_final: 0.7923 (ttm) REVERT: C 1107 ARG cc_start: 0.7596 (ttm170) cc_final: 0.7117 (ttm170) REVERT: C 1125 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8184 (p0) outliers start: 111 outliers final: 69 residues processed: 454 average time/residue: 0.1502 time to fit residues: 114.0780 Evaluate side-chains 427 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 352 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 295 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 181 optimal weight: 0.0980 chunk 290 optimal weight: 0.0980 chunk 280 optimal weight: 0.0980 chunk 154 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 804 GLN C 856 ASN C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.244775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.166139 restraints weight = 66557.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164323 restraints weight = 29883.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.169068 restraints weight = 18818.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170326 restraints weight = 13131.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170977 restraints weight = 11277.599| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 27314 Z= 0.103 Angle : 0.557 9.443 37255 Z= 0.276 Chirality : 0.045 0.334 4289 Planarity : 0.004 0.054 4771 Dihedral : 4.118 54.671 3597 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 2.95 % Allowed : 21.99 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3314 helix: 2.14 (0.21), residues: 629 sheet: -0.09 (0.21), residues: 645 loop : -1.56 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 466 TYR 0.022 0.001 TYR A1067 PHE 0.019 0.001 PHE B 592 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (27253) covalent geometry : angle 0.54313 / 0.27 (37097) SS BOND : bond 0.00326 / 0.22 ( 25) SS BOND : angle 1.40869 / 1.12 ( 50) hydrogen bonds : bond 0.03627 / 2.38 ( 838) hydrogen bonds : angle 5.10971 / 3.59 ( 2316) link_BETA1-4 : bond 0.00460 / 0.21 ( 6) link_BETA1-4 : angle 2.07641 / 1.23 ( 18) link_NAG-ASN : bond 0.00477 / 0.34 ( 30) link_NAG-ASN : angle 2.23743 / 1.47 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 393 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9180 (ptt) cc_final: 0.8915 (ptt) REVERT: A 825 LYS cc_start: 0.8359 (tptp) cc_final: 0.8025 (tptp) REVERT: A 979 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 1107 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6982 (mpp-170) REVERT: B 508 TYR cc_start: 0.7591 (m-80) cc_final: 0.7160 (m-80) REVERT: B 512 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 533 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.4751 (tp) REVERT: B 790 LYS cc_start: 0.8800 (mttt) cc_final: 0.8418 (mtpp) REVERT: B 954 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: C 228 ASP cc_start: 0.6260 (m-30) cc_final: 0.5870 (m-30) REVERT: C 353 TRP cc_start: -0.1442 (OUTLIER) cc_final: -0.2122 (m-90) REVERT: C 385 THR cc_start: 0.2496 (OUTLIER) cc_final: 0.2276 (m) REVERT: C 697 MET cc_start: 0.8346 (mtt) cc_final: 0.7906 (mtp) REVERT: C 808 ASP cc_start: 0.8463 (t0) cc_final: 0.8033 (t0) REVERT: C 1029 MET cc_start: 0.8773 (tpp) cc_final: 0.8026 (ttt) REVERT: C 1125 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8168 (p0) REVERT: C 1139 ASP cc_start: 0.8113 (t0) cc_final: 0.7675 (t0) REVERT: D 3 GLN cc_start: 0.7138 (mt0) cc_final: 0.6918 (mt0) outliers start: 85 outliers final: 48 residues processed: 450 average time/residue: 0.1518 time to fit residues: 115.3926 Evaluate side-chains 426 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 273 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 267 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 774 GLN C 804 GLN C 856 ASN C 907 ASN C 935 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.240774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162919 restraints weight = 75696.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.157664 restraints weight = 32658.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.160273 restraints weight = 23806.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.162200 restraints weight = 16245.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163214 restraints weight = 13264.209| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27314 Z= 0.176 Angle : 0.599 10.020 37255 Z= 0.296 Chirality : 0.046 0.319 4289 Planarity : 0.004 0.087 4771 Dihedral : 4.187 53.231 3595 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.78 % Favored : 93.13 % Rotamer: Outliers : 3.32 % Allowed : 21.82 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3314 helix: 1.96 (0.21), residues: 634 sheet: -0.11 (0.21), residues: 631 loop : -1.60 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.023 0.001 TYR A1067 PHE 0.020 0.001 PHE C 275 TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (27253) covalent geometry : angle 0.58509 / 0.29 (37097) SS BOND : bond 0.00409 / 0.26 ( 25) SS BOND : angle 1.57430 / 1.22 ( 50) hydrogen bonds : bond 0.04077 / 2.66 ( 838) hydrogen bonds : angle 5.13962 / 3.61 ( 2316) link_BETA1-4 : bond 0.00454 / 0.20 ( 6) link_BETA1-4 : angle 1.93819 / 1.16 ( 18) link_NAG-ASN : bond 0.00441 / 0.30 ( 30) link_NAG-ASN : angle 2.28209 / 1.51 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 372 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.8972 (tp40) cc_final: 0.8771 (tp40) REVERT: A 731 MET cc_start: 0.9041 (ptt) cc_final: 0.8804 (ptt) REVERT: A 825 LYS cc_start: 0.8329 (tptp) cc_final: 0.8005 (tptp) REVERT: A 979 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: A 1107 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7115 (mpp-170) REVERT: B 457 ARG cc_start: 0.7930 (tpt-90) cc_final: 0.7693 (tpt-90) REVERT: B 508 TYR cc_start: 0.7685 (m-80) cc_final: 0.7323 (m-80) REVERT: B 512 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8717 (t) REVERT: B 533 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.4849 (tp) REVERT: B 541 PHE cc_start: 0.7545 (p90) cc_final: 0.7314 (p90) REVERT: B 790 LYS cc_start: 0.8806 (mttt) cc_final: 0.8297 (mttp) REVERT: C 228 ASP cc_start: 0.6288 (m-30) cc_final: 0.5921 (m-30) REVERT: C 353 TRP cc_start: -0.1536 (OUTLIER) cc_final: -0.2231 (m-90) REVERT: C 385 THR cc_start: 0.2635 (OUTLIER) cc_final: 0.2428 (m) REVERT: C 697 MET cc_start: 0.8417 (mtt) cc_final: 0.8151 (mtm) REVERT: C 808 ASP cc_start: 0.8432 (t0) cc_final: 0.8074 (t0) REVERT: C 904 TYR cc_start: 0.7901 (m-80) cc_final: 0.7669 (m-80) REVERT: C 996 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 1029 MET cc_start: 0.8783 (tpp) cc_final: 0.7992 (ttm) REVERT: C 1107 ARG cc_start: 0.7615 (ttm170) cc_final: 0.7117 (ttm170) REVERT: C 1125 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8224 (p0) REVERT: D 3 GLN cc_start: 0.7228 (mt0) cc_final: 0.6993 (mt0) outliers start: 96 outliers final: 68 residues processed: 436 average time/residue: 0.1421 time to fit residues: 104.1364 Evaluate side-chains 439 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 363 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 310 optimal weight: 0.6980 chunk 238 optimal weight: 0.5980 chunk 222 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 299 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.237318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.158293 restraints weight = 51944.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.155862 restraints weight = 25173.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.159043 restraints weight = 18033.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.160231 restraints weight = 13973.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.160792 restraints weight = 12056.876| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27314 Z= 0.183 Angle : 0.609 13.247 37255 Z= 0.300 Chirality : 0.046 0.328 4289 Planarity : 0.004 0.075 4771 Dihedral : 4.255 53.908 3594 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Rotamer: Outliers : 3.97 % Allowed : 21.65 % Favored : 74.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3314 helix: 1.92 (0.21), residues: 633 sheet: -0.12 (0.21), residues: 643 loop : -1.63 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.023 0.001 TYR A1067 PHE 0.018 0.001 PHE C 562 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (27253) covalent geometry : angle 0.59122 / 0.30 (37097) SS BOND : bond 0.00467 / 0.28 ( 25) SS BOND : angle 1.61393 / 1.22 ( 50) hydrogen bonds : bond 0.04072 / 2.67 ( 838) hydrogen bonds : angle 5.14053 / 3.61 ( 2316) link_BETA1-4 : bond 0.00430 / 0.20 ( 6) link_BETA1-4 : angle 2.02055 / 1.20 ( 18) link_NAG-ASN : bond 0.00443 / 0.31 ( 30) link_NAG-ASN : angle 2.64519 / 1.64 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 384 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.9010 (tp40) cc_final: 0.8778 (tp40) REVERT: A 731 MET cc_start: 0.9135 (ptt) cc_final: 0.8914 (ptt) REVERT: A 825 LYS cc_start: 0.8389 (tptp) cc_final: 0.8089 (tptp) REVERT: A 979 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 1067 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 1107 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7069 (mpp-170) REVERT: B 457 ARG cc_start: 0.7897 (tpt-90) cc_final: 0.7642 (tpt-90) REVERT: B 508 TYR cc_start: 0.7718 (m-80) cc_final: 0.7380 (m-80) REVERT: B 512 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8716 (t) REVERT: B 790 LYS cc_start: 0.8817 (mttt) cc_final: 0.8328 (mttp) REVERT: C 228 ASP cc_start: 0.6155 (m-30) cc_final: 0.5822 (m-30) REVERT: C 353 TRP cc_start: -0.1468 (OUTLIER) cc_final: -0.2138 (m-90) REVERT: C 697 MET cc_start: 0.8514 (mtt) cc_final: 0.8046 (mtp) REVERT: C 703 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8212 (p0) REVERT: C 803 SER cc_start: 0.8464 (m) cc_final: 0.8159 (p) REVERT: C 808 ASP cc_start: 0.8418 (t0) cc_final: 0.8081 (t0) REVERT: C 1029 MET cc_start: 0.8858 (tpp) cc_final: 0.8047 (ttm) REVERT: C 1107 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7107 (ttm170) REVERT: C 1125 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8226 (p0) REVERT: C 1139 ASP cc_start: 0.8160 (t0) cc_final: 0.7752 (t0) REVERT: D 3 GLN cc_start: 0.7234 (mt0) cc_final: 0.7010 (mt0) outliers start: 115 outliers final: 82 residues processed: 460 average time/residue: 0.1387 time to fit residues: 107.5329 Evaluate side-chains 457 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 368 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 2 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 320 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 0.0570 chunk 88 optimal weight: 0.5980 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 804 GLN C 856 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.239259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159568 restraints weight = 60361.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156467 restraints weight = 29389.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158974 restraints weight = 20246.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159878 restraints weight = 16548.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.162324 restraints weight = 13492.648| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27314 Z= 0.128 Angle : 0.595 14.669 37255 Z= 0.287 Chirality : 0.046 0.461 4289 Planarity : 0.004 0.065 4771 Dihedral : 4.146 54.176 3594 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 3.15 % Allowed : 22.27 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3314 helix: 2.06 (0.21), residues: 627 sheet: -0.03 (0.21), residues: 630 loop : -1.56 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.022 0.001 TYR A1067 PHE 0.016 0.001 PHE A 559 TRP 0.012 0.001 TRP B 104 HIS 0.009 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (27253) covalent geometry : angle 0.56962 / 0.28 (37097) SS BOND : bond 0.00392 / 0.25 ( 25) SS BOND : angle 1.46166 / 1.14 ( 50) hydrogen bonds : bond 0.03739 / 2.45 ( 838) hydrogen bonds : angle 5.02985 / 3.53 ( 2316) link_BETA1-4 : bond 0.00446 / 0.22 ( 6) link_BETA1-4 : angle 2.08653 / 1.24 ( 18) link_NAG-ASN : bond 0.00474 / 0.33 ( 30) link_NAG-ASN : angle 3.27957 / 1.96 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 381 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.8939 (tp40) cc_final: 0.8693 (tp40) REVERT: A 731 MET cc_start: 0.9072 (ptt) cc_final: 0.8824 (ptt) REVERT: A 825 LYS cc_start: 0.8346 (tptp) cc_final: 0.8020 (tptp) REVERT: A 979 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: A 1107 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7037 (mpp-170) REVERT: B 457 ARG cc_start: 0.7828 (tpt-90) cc_final: 0.7591 (tpt-90) REVERT: B 508 TYR cc_start: 0.7645 (m-80) cc_final: 0.7333 (m-80) REVERT: B 512 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8647 (t) REVERT: B 790 LYS cc_start: 0.8804 (mttt) cc_final: 0.8283 (mttp) REVERT: C 228 ASP cc_start: 0.6235 (m-30) cc_final: 0.5892 (m-30) REVERT: C 353 TRP cc_start: -0.1408 (OUTLIER) cc_final: -0.2070 (m-90) REVERT: C 697 MET cc_start: 0.8568 (mtt) cc_final: 0.8113 (mtp) REVERT: C 808 ASP cc_start: 0.8426 (t0) cc_final: 0.8074 (t0) REVERT: C 996 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8468 (mp) REVERT: C 1029 MET cc_start: 0.8794 (tpp) cc_final: 0.8038 (ttm) REVERT: C 1107 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7161 (ttm170) REVERT: C 1125 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8197 (p0) REVERT: C 1139 ASP cc_start: 0.8185 (t0) cc_final: 0.7769 (t0) REVERT: D 3 GLN cc_start: 0.7244 (mt0) cc_final: 0.7031 (mt0) outliers start: 91 outliers final: 74 residues processed: 448 average time/residue: 0.1421 time to fit residues: 107.0102 Evaluate side-chains 449 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 369 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 104 optimal weight: 2.9990 chunk 324 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 935 GLN C 282 ASN C 856 ASN C 907 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.232173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152892 restraints weight = 80552.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.150735 restraints weight = 33245.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.151366 restraints weight = 25968.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.153326 restraints weight = 19328.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.154923 restraints weight = 15365.024| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 27314 Z= 0.294 Angle : 0.721 13.373 37255 Z= 0.357 Chirality : 0.050 0.459 4289 Planarity : 0.005 0.075 4771 Dihedral : 4.634 56.138 3594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 3.70 % Allowed : 21.69 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3314 helix: 1.77 (0.22), residues: 608 sheet: -0.20 (0.21), residues: 620 loop : -1.71 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 454 TYR 0.024 0.002 TYR A1067 PHE 0.029 0.002 PHE A 855 TRP 0.026 0.002 TRP B 104 HIS 0.009 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (27253) covalent geometry : angle 0.69804 / 0.35 (37097) SS BOND : bond 0.00567 / 0.37 ( 25) SS BOND : angle 1.99483 / 1.50 ( 50) hydrogen bonds : bond 0.04890 / 3.21 ( 838) hydrogen bonds : angle 5.39448 / 3.79 ( 2316) link_BETA1-4 : bond 0.00337 / 0.16 ( 6) link_BETA1-4 : angle 2.03767 / 1.20 ( 18) link_NAG-ASN : bond 0.00570 / 0.35 ( 30) link_NAG-ASN : angle 3.38119 / 2.09 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 387 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8911 (t80) cc_final: 0.8009 (t80) REVERT: A 591 SER cc_start: 0.8639 (m) cc_final: 0.8269 (p) REVERT: A 644 GLN cc_start: 0.8993 (tp40) cc_final: 0.8723 (tp40) REVERT: A 731 MET cc_start: 0.9200 (ptt) cc_final: 0.8977 (ptt) REVERT: A 825 LYS cc_start: 0.8338 (tptp) cc_final: 0.8025 (tptp) REVERT: A 979 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 1067 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 206 LYS cc_start: 0.8139 (tptt) cc_final: 0.7512 (tptm) REVERT: B 224 GLU cc_start: 0.6903 (mp0) cc_final: 0.5880 (mp0) REVERT: B 508 TYR cc_start: 0.7850 (m-80) cc_final: 0.7598 (m-80) REVERT: B 512 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 790 LYS cc_start: 0.8801 (mttt) cc_final: 0.8288 (mttp) REVERT: B 969 ASN cc_start: 0.8916 (p0) cc_final: 0.8646 (p0) REVERT: C 220 PHE cc_start: 0.3546 (OUTLIER) cc_final: 0.3075 (m-80) REVERT: C 228 ASP cc_start: 0.6609 (m-30) cc_final: 0.6292 (m-30) REVERT: C 321 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8848 (mm-40) REVERT: C 353 TRP cc_start: -0.0998 (OUTLIER) cc_final: -0.1686 (m-90) REVERT: C 661 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 697 MET cc_start: 0.8599 (mtt) cc_final: 0.8199 (mtp) REVERT: C 703 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8136 (p0) REVERT: C 756 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 779 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7672 (tt0) REVERT: C 786 LYS cc_start: 0.8347 (pttt) cc_final: 0.8080 (pttt) REVERT: C 808 ASP cc_start: 0.8434 (t0) cc_final: 0.8077 (t0) REVERT: C 878 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9023 (tt) REVERT: C 904 TYR cc_start: 0.8151 (m-10) cc_final: 0.7851 (m-10) REVERT: C 996 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8534 (mp) REVERT: C 1029 MET cc_start: 0.8868 (tpp) cc_final: 0.8158 (ttm) REVERT: C 1107 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7048 (ttm170) REVERT: C 1125 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8132 (p0) REVERT: C 1139 ASP cc_start: 0.8355 (t0) cc_final: 0.7967 (t0) outliers start: 107 outliers final: 76 residues processed: 462 average time/residue: 0.1487 time to fit residues: 115.2354 Evaluate side-chains 462 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 376 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 311 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 804 GLN C 856 ASN C 907 ASN ** C1010 GLN ** 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 = 0.4434 r_free = 0.4434 target = 0.234651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.159832 restraints weight = 82570.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153668 restraints weight = 34341.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.155147 restraints weight = 25096.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.156846 restraints weight = 17663.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.158274 restraints weight = 14354.095| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27314 Z= 0.205 Angle : 0.647 12.472 37255 Z= 0.317 Chirality : 0.048 0.386 4289 Planarity : 0.004 0.069 4771 Dihedral : 4.509 56.032 3594 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.50 % Rotamer: Outliers : 3.29 % Allowed : 22.47 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3314 helix: 1.79 (0.21), residues: 620 sheet: -0.22 (0.21), residues: 625 loop : -1.69 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.025 0.001 TYR A1067 PHE 0.020 0.001 PHE A 855 TRP 0.019 0.001 TRP B 104 HIS 0.008 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (27253) covalent geometry : angle 0.62352 / 0.31 (37097) SS BOND : bond 0.00544 / 0.35 ( 25) SS BOND : angle 1.77816 / 1.35 ( 50) hydrogen bonds : bond 0.04287 / 2.81 ( 838) hydrogen bonds : angle 5.25391 / 3.69 ( 2316) link_BETA1-4 : bond 0.00424 / 0.20 ( 6) link_BETA1-4 : angle 2.21819 / 1.29 ( 18) link_NAG-ASN : bond 0.00501 / 0.34 ( 30) link_NAG-ASN : angle 3.17686 / 1.96 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 395 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8875 (t80) cc_final: 0.7972 (t80) REVERT: A 591 SER cc_start: 0.8721 (m) cc_final: 0.8369 (p) REVERT: A 644 GLN cc_start: 0.8938 (tp40) cc_final: 0.8648 (tp40) REVERT: A 731 MET cc_start: 0.9167 (ptt) cc_final: 0.8938 (ptt) REVERT: A 825 LYS cc_start: 0.8282 (tptp) cc_final: 0.7955 (tptp) REVERT: A 979 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: A 1107 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7086 (mpp-170) REVERT: B 177 MET cc_start: 0.5486 (tpt) cc_final: 0.4732 (tpt) REVERT: B 206 LYS cc_start: 0.8019 (tptt) cc_final: 0.7391 (tptm) REVERT: B 224 GLU cc_start: 0.6815 (mp0) cc_final: 0.5801 (mp0) REVERT: B 327 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6936 (m) REVERT: B 508 TYR cc_start: 0.7752 (m-80) cc_final: 0.7507 (m-80) REVERT: B 512 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.8773 (t) REVERT: B 542 ASN cc_start: 0.7822 (t0) cc_final: 0.7281 (t0) REVERT: B 790 LYS cc_start: 0.8803 (mttt) cc_final: 0.8290 (mttp) REVERT: B 969 ASN cc_start: 0.8901 (p0) cc_final: 0.8637 (p0) REVERT: B 1107 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7926 (mtt-85) REVERT: C 220 PHE cc_start: 0.3718 (OUTLIER) cc_final: 0.2875 (m-80) REVERT: C 228 ASP cc_start: 0.6297 (m-30) cc_final: 0.5980 (m-30) REVERT: C 353 TRP cc_start: -0.1171 (OUTLIER) cc_final: -0.1860 (m-90) REVERT: C 661 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7912 (pt0) REVERT: C 697 MET cc_start: 0.8631 (mtt) cc_final: 0.8144 (mtp) REVERT: C 703 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (p0) REVERT: C 756 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 779 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7625 (tt0) REVERT: C 808 ASP cc_start: 0.8457 (t0) cc_final: 0.8084 (t0) REVERT: C 904 TYR cc_start: 0.8090 (m-10) cc_final: 0.7619 (m-10) REVERT: C 996 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 1029 MET cc_start: 0.8777 (tpp) cc_final: 0.8089 (ttt) REVERT: C 1107 ARG cc_start: 0.7661 (ttm170) cc_final: 0.7124 (ttm170) REVERT: C 1125 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8246 (p0) REVERT: C 1139 ASP cc_start: 0.8324 (t0) cc_final: 0.7935 (t0) REVERT: D 3 GLN cc_start: 0.7073 (mt0) cc_final: 0.6795 (mt0) outliers start: 95 outliers final: 75 residues processed: 462 average time/residue: 0.1484 time to fit residues: 114.6348 Evaluate side-chains 471 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 386 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 329 optimal weight: 0.8980 chunk 246 optimal weight: 20.0000 chunk 256 optimal weight: 50.0000 chunk 54 optimal weight: 0.7980 chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 202 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 245 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 856 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.236792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.156092 restraints weight = 62735.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.154157 restraints weight = 28690.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.157522 restraints weight = 18785.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.158535 restraints weight = 14386.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.159099 restraints weight = 12222.002| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27314 Z= 0.143 Angle : 0.614 10.642 37255 Z= 0.299 Chirality : 0.046 0.347 4289 Planarity : 0.004 0.061 4771 Dihedral : 4.314 55.512 3594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 2.88 % Allowed : 23.26 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3314 helix: 1.93 (0.22), residues: 621 sheet: -0.09 (0.21), residues: 611 loop : -1.65 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.023 0.001 TYR A1067 PHE 0.016 0.001 PHE C 562 TRP 0.013 0.001 TRP B 104 HIS 0.008 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (27253) covalent geometry : angle 0.59393 / 0.29 (37097) SS BOND : bond 0.00466 / 0.31 ( 25) SS BOND : angle 1.61554 / 1.24 ( 50) hydrogen bonds : bond 0.03886 / 2.54 ( 838) hydrogen bonds : angle 5.10065 / 3.59 ( 2316) link_BETA1-4 : bond 0.00424 / 0.21 ( 6) link_BETA1-4 : angle 2.20950 / 1.29 ( 18) link_NAG-ASN : bond 0.00481 / 0.33 ( 30) link_NAG-ASN : angle 2.88291 / 1.80 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 390 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8830 (t80) cc_final: 0.7877 (t80) REVERT: A 487 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6332 (t0) REVERT: A 644 GLN cc_start: 0.8954 (tp40) cc_final: 0.8670 (tp40) REVERT: A 731 MET cc_start: 0.9106 (ptt) cc_final: 0.8864 (ptt) REVERT: A 825 LYS cc_start: 0.8297 (tptp) cc_final: 0.7994 (tptp) REVERT: A 979 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: A 1107 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7140 (mpp-170) REVERT: B 206 LYS cc_start: 0.8012 (tptt) cc_final: 0.7394 (tptm) REVERT: B 224 GLU cc_start: 0.6755 (mp0) cc_final: 0.5759 (mp0) REVERT: B 457 ARG cc_start: 0.7668 (tpt-90) cc_final: 0.7261 (ttt-90) REVERT: B 508 TYR cc_start: 0.7718 (m-80) cc_final: 0.7443 (m-80) REVERT: B 512 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8632 (t) REVERT: B 542 ASN cc_start: 0.7574 (t0) cc_final: 0.7101 (t0) REVERT: B 655 HIS cc_start: 0.8954 (t-170) cc_final: 0.8690 (t-90) REVERT: B 790 LYS cc_start: 0.8781 (mttt) cc_final: 0.8283 (mttp) REVERT: B 825 LYS cc_start: 0.8249 (mmmt) cc_final: 0.8045 (mmmt) REVERT: B 1107 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7866 (mtt-85) REVERT: C 228 ASP cc_start: 0.6211 (m-30) cc_final: 0.5867 (m-30) REVERT: C 280 ASN cc_start: 0.7969 (t0) cc_final: 0.7668 (t0) REVERT: C 353 TRP cc_start: -0.1263 (OUTLIER) cc_final: -0.1883 (m-90) REVERT: C 756 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 779 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7454 (tt0) REVERT: C 808 ASP cc_start: 0.8437 (t0) cc_final: 0.8043 (t0) REVERT: C 904 TYR cc_start: 0.8126 (m-10) cc_final: 0.7695 (m-10) REVERT: C 996 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 1029 MET cc_start: 0.8791 (tpp) cc_final: 0.8053 (ttt) REVERT: C 1107 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7232 (ttm170) REVERT: C 1125 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8207 (p0) REVERT: C 1139 ASP cc_start: 0.8290 (t0) cc_final: 0.7889 (t0) outliers start: 83 outliers final: 67 residues processed: 450 average time/residue: 0.1514 time to fit residues: 113.9338 Evaluate side-chains 453 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 378 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 204 optimal weight: 0.6980 chunk 237 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 261 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.237256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156351 restraints weight = 62533.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.154135 restraints weight = 28030.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.156199 restraints weight = 20528.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.157390 restraints weight = 16034.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.158643 restraints weight = 13495.814| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27314 Z= 0.138 Angle : 0.607 10.067 37255 Z= 0.295 Chirality : 0.046 0.345 4289 Planarity : 0.004 0.060 4771 Dihedral : 4.273 55.567 3594 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.56 % Rotamer: Outliers : 2.81 % Allowed : 23.12 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3314 helix: 1.98 (0.22), residues: 620 sheet: -0.08 (0.21), residues: 617 loop : -1.62 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.023 0.001 TYR A1067 PHE 0.016 0.001 PHE A 559 TRP 0.013 0.001 TRP B 104 HIS 0.008 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (27253) covalent geometry : angle 0.58799 / 0.29 (37097) SS BOND : bond 0.00433 / 0.28 ( 25) SS BOND : angle 1.56685 / 1.20 ( 50) hydrogen bonds : bond 0.03826 / 2.50 ( 838) hydrogen bonds : angle 5.06295 / 3.57 ( 2316) link_BETA1-4 : bond 0.00415 / 0.20 ( 6) link_BETA1-4 : angle 2.16278 / 1.28 ( 18) link_NAG-ASN : bond 0.00474 / 0.32 ( 30) link_NAG-ASN : angle 2.78427 / 1.75 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5590.93 seconds wall clock time: 96 minutes 51.87 seconds (5811.87 seconds total)