Starting phenix.real_space_refine on Sun Jul 5 23:23:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz6_26880/07_2026/7uz6_26880.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19689 2.51 5 N 5106 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 30942 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 7.10, per 1000 atoms: 0.23 Number of scatterers: 30942 At special positions: 0 Unit cell: (153.088, 151.424, 189.696, 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 132 16.00 O 6015 8.00 N 5106 7.00 C 19689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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 NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 234 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 282 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7302 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 71 sheets defined 21.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.263A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.302A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.619A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.591A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 1033 removed outlier: 4.472A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.631A pdb=" N THR B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.136A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.732A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.588A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.592A 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 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.578A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.609A pdb=" N THR C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.131A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.667A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A 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 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.096A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.461A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.090A pdb=" N TYR H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.129A pdb=" N ILE L 99 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'N' and resid 95 through 100 removed outlier: 3.504A pdb=" N ILE N 99 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA N 100 " --> pdb=" O GLU N 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 removed outlier: 3.564A pdb=" N SER P 99 " --> pdb=" O SER P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.739A pdb=" N ILE Q 99 " --> pdb=" O SER Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.898A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.899A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.965A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.036A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.236A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.805A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.587A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.603A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.881A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.584A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.042A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.540A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.209A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.731A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.614A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.740A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.161A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.760A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.201A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.711A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.706A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.539A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.196A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.575A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AF9, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.952A pdb=" N ASP L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER L 83 " --> pdb=" O ASP L 86 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.591A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.789A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.613A pdb=" N THR M 77 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 65 through 67 removed outlier: 6.897A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP N 86 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 83 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'N' and resid 66 through 67 removed outlier: 6.851A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE N 39 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'P' and resid 64 through 67 removed outlier: 3.505A pdb=" N PHE P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR P 66 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP P 41 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP P 55 " --> pdb=" O ILE P 39 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE P 39 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 42 " --> pdb=" O TYR P 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP Q 86 " --> pdb=" O SER Q 83 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Q 83 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE Q 39 " --> pdb=" O LYS Q 55 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3171 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: 9.31 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9921 1.35 - 1.47: 8210 1.47 - 1.59: 13386 1.59 - 1.72: 1 1.72 - 1.84: 168 Bond restraints: 31686 Sorted by residual: bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" CB PRO B 230 " pdb=" CG PRO B 230 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 ... (remaining 31681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 41670 1.35 - 2.70: 1205 2.70 - 4.06: 262 4.06 - 5.41: 37 5.41 - 6.76: 8 Bond angle restraints: 43182 Sorted by residual: angle pdb=" N VAL B 127 " pdb=" CA VAL B 127 " pdb=" C VAL B 127 " ideal model delta sigma weight residual 106.21 110.32 -4.11 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 106.21 110.05 -3.84 1.07e+00 8.73e-01 1.29e+01 angle pdb=" N GLY A1124 " pdb=" CA GLY A1124 " pdb=" C GLY A1124 " ideal model delta sigma weight residual 111.21 114.92 -3.71 1.04e+00 9.25e-01 1.28e+01 angle pdb=" C ARG A 102 " pdb=" N GLY A 103 " pdb=" CA GLY A 103 " ideal model delta sigma weight residual 122.03 117.66 4.37 1.28e+00 6.10e-01 1.17e+01 angle pdb=" N GLY C1124 " pdb=" CA GLY C1124 " pdb=" C GLY C1124 " ideal model delta sigma weight residual 111.21 114.74 -3.53 1.04e+00 9.25e-01 1.15e+01 ... (remaining 43177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 16848 17.46 - 34.92: 1321 34.92 - 52.38: 211 52.38 - 69.84: 39 69.84 - 87.30: 31 Dihedral angle restraints: 18450 sinusoidal: 7083 harmonic: 11367 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -24.51 -61.49 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 153.52 -60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -34.74 -51.26 1 1.00e+01 1.00e-02 3.59e+01 ... (remaining 18447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4290 0.065 - 0.130: 664 0.130 - 0.195: 8 0.195 - 0.260: 3 0.260 - 0.325: 6 Chirality restraints: 4971 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4968 not shown) Planarity restraints: 5583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO L 50 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 49 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO N 50 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 50 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.015 2.00e-02 2.50e+03 1.52e-02 4.07e+00 pdb=" CG PHE A 906 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 5580 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 315 2.62 - 3.19: 27230 3.19 - 3.76: 47629 3.76 - 4.33: 67680 4.33 - 4.90: 113970 Nonbonded interactions: 256824 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.055 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.199 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 155 " pdb=" NH1 ARG A 246 " model vdw 2.209 3.120 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.212 3.040 ... (remaining 256819 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.030 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.107 31767 Z= 0.170 Angle : 0.592 11.991 43383 Z= 0.307 Chirality : 0.045 0.325 4971 Planarity : 0.004 0.096 5544 Dihedral : 13.072 87.301 11022 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.38 (0.13), residues: 3864 helix: 1.46 (0.20), residues: 731 sheet: -0.08 (0.16), residues: 1004 loop : -0.95 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 190 TYR 0.021 0.001 TYR B 636 PHE 0.035 0.001 PHE A 906 TRP 0.022 0.001 TRP C 258 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (31686) covalent geometry : angle 0.56344 / 0.30 (43182) SS BOND : bond 0.00389 / 0.22 ( 42) SS BOND : angle 0.90044 / 0.68 ( 84) hydrogen bonds : bond 0.20173 / 13.30 ( 1131) hydrogen bonds : angle 8.74157 / 6.13 ( 3171) link_NAG-ASN : bond 0.00733 / 0.47 ( 39) link_NAG-ASN : angle 3.49979 / 2.48 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.215 Fit side-chains REVERT: A 153 MET cc_start: 0.7049 (tpt) cc_final: 0.6755 (ptt) REVERT: A 495 TYR cc_start: 0.6814 (t80) cc_final: 0.6544 (t80) REVERT: A 1123 SER cc_start: 0.8614 (m) cc_final: 0.8340 (m) REVERT: B 463 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: H 89 MET cc_start: 0.4529 (ppp) cc_final: 0.3804 (ppp) REVERT: M 21 MET cc_start: 0.6675 (mmt) cc_final: 0.6117 (mpt) REVERT: M 43 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6882 (ttmm) REVERT: N 91 ILE cc_start: 0.6764 (mt) cc_final: 0.6549 (pt) REVERT: P 21 MET cc_start: 0.6663 (mmt) cc_final: 0.6179 (mpt) REVERT: P 89 MET cc_start: 0.4287 (ppp) cc_final: 0.3850 (ppp) REVERT: P 108 ASP cc_start: 0.7173 (t70) cc_final: 0.6951 (t70) REVERT: P 113 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7157 (ptp-110) outliers start: 1 outliers final: 3 residues processed: 377 average time/residue: 0.5822 time to fit residues: 264.4384 Evaluate side-chains 265 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 422 ASN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN H 36 HIS L 6 GLN L 108 ASN N 108 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.195780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117593 restraints weight = 38657.308| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.62 r_work: 0.3310 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 31767 Z= 0.243 Angle : 0.654 12.208 43383 Z= 0.330 Chirality : 0.049 0.329 4971 Planarity : 0.005 0.071 5544 Dihedral : 4.470 27.536 4203 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.52 % Allowed : 7.63 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.42 (0.13), residues: 3864 helix: 1.63 (0.20), residues: 681 sheet: -0.19 (0.16), residues: 1011 loop : -0.95 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 45 TYR 0.034 0.002 TYR H 109 PHE 0.035 0.002 PHE A 906 TRP 0.016 0.002 TRP B 886 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (31686) covalent geometry : angle 0.62526 / 0.32 (43182) SS BOND : bond 0.00707 / 0.42 ( 42) SS BOND : angle 1.11406 / 0.81 ( 84) hydrogen bonds : bond 0.04866 / 3.27 ( 1131) hydrogen bonds : angle 6.63392 / 4.61 ( 3171) link_NAG-ASN : bond 0.00780 / 0.50 ( 39) link_NAG-ASN : angle 3.64138 / 2.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7250 (tpt) cc_final: 0.6664 (ptt) REVERT: A 290 ASP cc_start: 0.7487 (t0) cc_final: 0.7224 (t0) REVERT: A 495 TYR cc_start: 0.6911 (t80) cc_final: 0.6632 (t80) REVERT: B 324 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5847 (pt0) REVERT: C 153 MET cc_start: 0.6873 (pp-130) cc_final: 0.5748 (pmm) REVERT: C 290 ASP cc_start: 0.7756 (t0) cc_final: 0.7498 (t0) REVERT: C 309 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: C 615 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7820 (m) REVERT: C 994 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8119 (t0) REVERT: H 89 MET cc_start: 0.3869 (ppp) cc_final: 0.3447 (ppp) REVERT: M 21 MET cc_start: 0.5864 (mmt) cc_final: 0.5454 (mpt) REVERT: M 40 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (p) REVERT: M 113 ARG cc_start: 0.7743 (mpp-170) cc_final: 0.7210 (ptp-110) REVERT: P 21 MET cc_start: 0.6135 (mmt) cc_final: 0.5483 (mmm) REVERT: P 41 TRP cc_start: 0.5446 (m100) cc_final: 0.5204 (m100) REVERT: P 89 MET cc_start: 0.4085 (ppp) cc_final: 0.3844 (ppp) REVERT: P 108 ASP cc_start: 0.7281 (t70) cc_final: 0.7006 (t70) REVERT: Q 39 ILE cc_start: 0.7781 (mm) cc_final: 0.7574 (mm) outliers start: 51 outliers final: 25 residues processed: 326 average time/residue: 0.5230 time to fit residues: 208.7541 Evaluate side-chains 308 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain M residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 81 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 329 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 36 HIS ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117416 restraints weight = 38541.330| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.62 r_work: 0.3306 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31767 Z= 0.220 Angle : 0.621 12.421 43383 Z= 0.312 Chirality : 0.048 0.327 4971 Planarity : 0.004 0.056 5544 Dihedral : 4.484 26.283 4197 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.38 % Allowed : 10.31 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.46 (0.13), residues: 3864 helix: 1.69 (0.20), residues: 681 sheet: -0.37 (0.16), residues: 1041 loop : -0.93 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 190 TYR 0.035 0.002 TYR M 109 PHE 0.028 0.002 PHE A 906 TRP 0.019 0.002 TRP P 38 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (31686) covalent geometry : angle 0.59141 / 0.31 (43182) SS BOND : bond 0.00618 / 0.35 ( 42) SS BOND : angle 1.05760 / 0.78 ( 84) hydrogen bonds : bond 0.04605 / 3.10 ( 1131) hydrogen bonds : angle 6.29856 / 4.36 ( 3171) link_NAG-ASN : bond 0.00731 / 0.46 ( 39) link_NAG-ASN : angle 3.63484 / 2.57 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7162 (tpt) cc_final: 0.6637 (ptt) REVERT: A 273 ARG cc_start: 0.6025 (mtt-85) cc_final: 0.5532 (mmm-85) REVERT: A 357 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7801 (ptm160) REVERT: A 495 TYR cc_start: 0.6925 (t80) cc_final: 0.6636 (t80) REVERT: A 675 GLN cc_start: 0.7808 (mt0) cc_final: 0.6859 (pp30) REVERT: A 756 TYR cc_start: 0.7603 (t80) cc_final: 0.7080 (m-80) REVERT: C 153 MET cc_start: 0.6989 (pp-130) cc_final: 0.5766 (pmm) REVERT: C 290 ASP cc_start: 0.7839 (t0) cc_final: 0.7572 (t0) REVERT: C 309 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: C 495 TYR cc_start: 0.7172 (t80) cc_final: 0.6616 (t80) REVERT: C 994 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8108 (t0) REVERT: H 21 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.5170 (mpt) REVERT: H 43 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7053 (ttmm) REVERT: H 89 MET cc_start: 0.3956 (ppp) cc_final: 0.3195 (ppp) REVERT: M 21 MET cc_start: 0.5842 (mmt) cc_final: 0.5480 (mpt) REVERT: M 40 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7990 (p) REVERT: M 43 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6834 (ttmm) REVERT: M 109 TYR cc_start: 0.7929 (t80) cc_final: 0.7532 (t80) REVERT: M 113 ARG cc_start: 0.7747 (mpp-170) cc_final: 0.7100 (ptp-110) REVERT: P 21 MET cc_start: 0.5951 (mmt) cc_final: 0.5608 (mmm) REVERT: P 89 MET cc_start: 0.3868 (ppp) cc_final: 0.3642 (ppp) REVERT: P 108 ASP cc_start: 0.7263 (t70) cc_final: 0.6870 (t70) REVERT: P 113 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6647 (ptp-110) REVERT: Q 42 TYR cc_start: 0.6358 (m-10) cc_final: 0.6137 (m-10) outliers start: 80 outliers final: 35 residues processed: 339 average time/residue: 0.5451 time to fit residues: 225.8470 Evaluate side-chains 305 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN Q 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117771 restraints weight = 38132.500| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.59 r_work: 0.3306 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31767 Z= 0.179 Angle : 0.601 12.316 43383 Z= 0.301 Chirality : 0.047 0.327 4971 Planarity : 0.004 0.054 5544 Dihedral : 4.449 29.848 4197 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 11.97 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.44 (0.13), residues: 3864 helix: 1.82 (0.20), residues: 681 sheet: -0.33 (0.16), residues: 1033 loop : -0.97 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 346 TYR 0.025 0.001 TYR H 109 PHE 0.016 0.001 PHE A 906 TRP 0.012 0.001 TRP H 38 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (31686) covalent geometry : angle 0.57040 / 0.29 (43182) SS BOND : bond 0.00616 / 0.39 ( 42) SS BOND : angle 1.27357 / 0.84 ( 84) hydrogen bonds : bond 0.04191 / 2.83 ( 1131) hydrogen bonds : angle 6.10721 / 4.22 ( 3171) link_NAG-ASN : bond 0.00740 / 0.46 ( 39) link_NAG-ASN : angle 3.58044 / 2.54 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7100 (tpt) cc_final: 0.6621 (ptt) REVERT: A 177 MET cc_start: 0.6024 (ppp) cc_final: 0.5101 (ppp) REVERT: A 273 ARG cc_start: 0.5944 (mtt-85) cc_final: 0.5555 (mmm-85) REVERT: A 357 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7729 (ptm160) REVERT: A 495 TYR cc_start: 0.6887 (t80) cc_final: 0.6588 (t80) REVERT: A 564 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: A 574 ASP cc_start: 0.7746 (t0) cc_final: 0.7355 (t0) REVERT: A 675 GLN cc_start: 0.7741 (mt0) cc_final: 0.6762 (pp30) REVERT: A 756 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: B 534 VAL cc_start: 0.8194 (t) cc_final: 0.7865 (m) REVERT: B 675 GLN cc_start: 0.7639 (mt0) cc_final: 0.6547 (pp30) REVERT: C 153 MET cc_start: 0.6999 (pp-130) cc_final: 0.5813 (pmm) REVERT: C 177 MET cc_start: 0.5902 (mtp) cc_final: 0.5595 (mpp) REVERT: C 309 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: C 495 TYR cc_start: 0.7156 (t80) cc_final: 0.6572 (t80) REVERT: C 994 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (t0) REVERT: C 1092 GLU cc_start: 0.8409 (tp30) cc_final: 0.7485 (pt0) REVERT: H 21 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5210 (mpt) REVERT: H 43 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6960 (ttmm) REVERT: H 89 MET cc_start: 0.3925 (ppp) cc_final: 0.3107 (ppp) REVERT: M 21 MET cc_start: 0.5756 (mmt) cc_final: 0.5424 (mpt) REVERT: M 43 LYS cc_start: 0.7053 (ttpp) cc_final: 0.6675 (ttmm) REVERT: M 113 ARG cc_start: 0.7692 (mpp-170) cc_final: 0.7057 (ptp-110) REVERT: N 27 GLN cc_start: 0.7843 (mp-120) cc_final: 0.7423 (mp10) REVERT: P 89 MET cc_start: 0.4014 (ppp) cc_final: 0.3579 (ppp) REVERT: P 108 ASP cc_start: 0.7202 (t70) cc_final: 0.6893 (t70) REVERT: Q 42 TYR cc_start: 0.6337 (m-10) cc_final: 0.6119 (m-10) outliers start: 85 outliers final: 33 residues processed: 332 average time/residue: 0.5426 time to fit residues: 222.2706 Evaluate side-chains 313 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 22 optimal weight: 40.0000 chunk 313 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 339 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 329 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS L 108 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.196004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118332 restraints weight = 38412.246| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.63 r_work: 0.3320 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31767 Z= 0.150 Angle : 0.580 12.252 43383 Z= 0.289 Chirality : 0.046 0.326 4971 Planarity : 0.004 0.054 5544 Dihedral : 4.371 29.024 4197 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 2.32 % Allowed : 13.20 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.40 (0.13), residues: 3864 helix: 1.95 (0.20), residues: 681 sheet: -0.39 (0.16), residues: 1051 loop : -0.94 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 45 TYR 0.025 0.001 TYR A 453 PHE 0.015 0.001 PHE A 898 TRP 0.011 0.001 TRP B 886 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (31686) covalent geometry : angle 0.55047 / 0.28 (43182) SS BOND : bond 0.00450 / 0.25 ( 42) SS BOND : angle 0.97538 / 0.69 ( 84) hydrogen bonds : bond 0.03937 / 2.66 ( 1131) hydrogen bonds : angle 5.95367 / 4.11 ( 3171) link_NAG-ASN : bond 0.00733 / 0.46 ( 39) link_NAG-ASN : angle 3.49326 / 2.49 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 277 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6938 (tmtt) cc_final: 0.6505 (tptp) REVERT: A 153 MET cc_start: 0.7020 (tpt) cc_final: 0.6580 (ptt) REVERT: A 177 MET cc_start: 0.5938 (ppp) cc_final: 0.4797 (ppp) REVERT: A 233 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5707 (mt) REVERT: A 273 ARG cc_start: 0.5910 (mtt-85) cc_final: 0.5542 (mmm-85) REVERT: A 357 ARG cc_start: 0.8363 (ttp80) cc_final: 0.7741 (ptm160) REVERT: A 467 ASP cc_start: 0.7540 (t70) cc_final: 0.7133 (t0) REVERT: A 495 TYR cc_start: 0.6911 (t80) cc_final: 0.6601 (t80) REVERT: A 574 ASP cc_start: 0.7778 (t0) cc_final: 0.7355 (t0) REVERT: A 675 GLN cc_start: 0.7710 (mt0) cc_final: 0.6771 (pp30) REVERT: A 756 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7098 (m-80) REVERT: B 170 TYR cc_start: 0.5659 (t80) cc_final: 0.5243 (t80) REVERT: B 661 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 675 GLN cc_start: 0.7610 (mt0) cc_final: 0.6531 (pp30) REVERT: B 994 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8019 (t0) REVERT: C 153 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.5829 (pmm) REVERT: C 495 TYR cc_start: 0.7182 (t80) cc_final: 0.6595 (t80) REVERT: C 994 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8022 (t0) REVERT: C 1092 GLU cc_start: 0.8344 (tp30) cc_final: 0.7481 (pt0) REVERT: C 1144 GLU cc_start: 0.8562 (mp0) cc_final: 0.8117 (mp0) REVERT: H 39 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.7995 (tp) REVERT: H 43 LYS cc_start: 0.7344 (ttpp) cc_final: 0.6977 (ttmm) REVERT: L 42 TYR cc_start: 0.5657 (OUTLIER) cc_final: 0.5331 (m-80) REVERT: M 21 MET cc_start: 0.5780 (mmt) cc_final: 0.5479 (mpt) REVERT: M 43 LYS cc_start: 0.7052 (ttpp) cc_final: 0.6644 (ttmm) REVERT: M 113 ARG cc_start: 0.7646 (mpp-170) cc_final: 0.7091 (ptp-110) REVERT: N 27 GLN cc_start: 0.7844 (mp-120) cc_final: 0.7455 (mp10) REVERT: P 89 MET cc_start: 0.4104 (ppp) cc_final: 0.3640 (ppp) REVERT: P 108 ASP cc_start: 0.7270 (t70) cc_final: 0.6841 (t70) REVERT: P 113 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6658 (ptp-110) outliers start: 78 outliers final: 33 residues processed: 322 average time/residue: 0.5475 time to fit residues: 216.5374 Evaluate side-chains 304 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 42 TYR Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 78 optimal weight: 0.0370 chunk 15 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 353 optimal weight: 6.9990 chunk 260 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1010 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.199982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123811 restraints weight = 38455.766| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.63 r_work: 0.3369 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31767 Z= 0.127 Angle : 0.567 12.255 43383 Z= 0.281 Chirality : 0.045 0.325 4971 Planarity : 0.004 0.053 5544 Dihedral : 4.252 28.336 4197 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 2.47 % Allowed : 13.67 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.30 (0.13), residues: 3864 helix: 2.11 (0.20), residues: 681 sheet: -0.27 (0.16), residues: 1015 loop : -0.92 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 45 TYR 0.026 0.001 TYR A 453 PHE 0.018 0.001 PHE M 71 TRP 0.010 0.001 TRP H 38 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (31686) covalent geometry : angle 0.53850 / 0.27 (43182) SS BOND : bond 0.00368 / 0.21 ( 42) SS BOND : angle 0.90010 / 0.65 ( 84) hydrogen bonds : bond 0.03690 / 2.49 ( 1131) hydrogen bonds : angle 5.77489 / 3.98 ( 3171) link_NAG-ASN : bond 0.00726 / 0.45 ( 39) link_NAG-ASN : angle 3.40263 / 2.43 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 282 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6984 (tpt) cc_final: 0.6564 (ptt) REVERT: A 177 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.4865 (ppp) REVERT: A 233 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5484 (mt) REVERT: A 273 ARG cc_start: 0.5907 (mtt-85) cc_final: 0.5460 (mmm-85) REVERT: A 357 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7686 (ptm160) REVERT: A 467 ASP cc_start: 0.7548 (t70) cc_final: 0.7135 (t0) REVERT: A 495 TYR cc_start: 0.6880 (t80) cc_final: 0.6554 (t80) REVERT: A 564 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: A 574 ASP cc_start: 0.7774 (t0) cc_final: 0.7356 (t0) REVERT: A 675 GLN cc_start: 0.7674 (mt0) cc_final: 0.6746 (pp30) REVERT: A 756 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: A 868 GLU cc_start: 0.8005 (tt0) cc_final: 0.7199 (tp30) REVERT: A 1092 GLU cc_start: 0.8269 (tp30) cc_final: 0.7239 (pt0) REVERT: B 168 PHE cc_start: 0.3427 (t80) cc_final: 0.3214 (t80) REVERT: B 170 TYR cc_start: 0.5649 (t80) cc_final: 0.5260 (t80) REVERT: B 235 ILE cc_start: 0.6847 (mm) cc_final: 0.6621 (mm) REVERT: B 237 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.6171 (mpp80) REVERT: B 994 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.8000 (t0) REVERT: C 153 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.5919 (pmm) REVERT: C 309 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: C 495 TYR cc_start: 0.7169 (t80) cc_final: 0.6531 (t80) REVERT: C 994 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7981 (t0) REVERT: C 1092 GLU cc_start: 0.8286 (tp30) cc_final: 0.7477 (pt0) REVERT: C 1094 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7436 (p) REVERT: C 1144 GLU cc_start: 0.8573 (mp0) cc_final: 0.8211 (mp0) REVERT: H 39 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8013 (tp) REVERT: H 43 LYS cc_start: 0.7201 (ttpp) cc_final: 0.6767 (ttmm) REVERT: H 45 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8072 (mmt90) REVERT: L 42 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: L 66 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: M 21 MET cc_start: 0.5749 (mmt) cc_final: 0.5394 (mpt) REVERT: M 43 LYS cc_start: 0.7034 (ttpp) cc_final: 0.6637 (ttmm) REVERT: M 45 ARG cc_start: 0.8867 (mtp-110) cc_final: 0.8609 (mtp-110) REVERT: M 113 ARG cc_start: 0.7623 (mpp-170) cc_final: 0.7293 (ptp-110) REVERT: P 43 LYS cc_start: 0.7078 (tttt) cc_final: 0.6554 (tmtt) REVERT: P 89 MET cc_start: 0.4027 (ppp) cc_final: 0.3470 (ppp) REVERT: P 108 ASP cc_start: 0.7235 (t70) cc_final: 0.6863 (t70) outliers start: 83 outliers final: 37 residues processed: 333 average time/residue: 0.5320 time to fit residues: 217.8850 Evaluate side-chains 314 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain L residue 42 TYR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129029 restraints weight = 38837.641| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.08 r_work: 0.3283 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31767 Z= 0.166 Angle : 0.585 12.107 43383 Z= 0.290 Chirality : 0.046 0.329 4971 Planarity : 0.004 0.056 5544 Dihedral : 4.283 28.074 4197 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 14.09 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.33 (0.13), residues: 3864 helix: 2.11 (0.20), residues: 673 sheet: -0.33 (0.16), residues: 1021 loop : -0.91 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 466 TYR 0.023 0.001 TYR A 453 PHE 0.015 0.001 PHE P 71 TRP 0.011 0.001 TRP H 52 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (31686) covalent geometry : angle 0.55712 / 0.28 (43182) SS BOND : bond 0.00444 / 0.25 ( 42) SS BOND : angle 0.91559 / 0.65 ( 84) hydrogen bonds : bond 0.03883 / 2.62 ( 1131) hydrogen bonds : angle 5.77612 / 3.97 ( 3171) link_NAG-ASN : bond 0.00726 / 0.46 ( 39) link_NAG-ASN : angle 3.42968 / 2.45 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 279 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6976 (tmtt) cc_final: 0.6513 (tptp) REVERT: A 153 MET cc_start: 0.6974 (tpt) cc_final: 0.6565 (ptt) REVERT: A 177 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.4883 (ppp) REVERT: A 233 ILE cc_start: 0.5923 (OUTLIER) cc_final: 0.5542 (mt) REVERT: A 273 ARG cc_start: 0.5933 (mtt-85) cc_final: 0.5479 (mmm-85) REVERT: A 357 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7737 (ptm160) REVERT: A 467 ASP cc_start: 0.7531 (t70) cc_final: 0.7111 (t0) REVERT: A 495 TYR cc_start: 0.6971 (t80) cc_final: 0.6744 (t80) REVERT: A 564 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: A 574 ASP cc_start: 0.7792 (t0) cc_final: 0.7376 (t0) REVERT: A 756 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: A 1092 GLU cc_start: 0.8312 (tp30) cc_final: 0.7251 (pt0) REVERT: B 170 TYR cc_start: 0.5701 (t80) cc_final: 0.5311 (t80) REVERT: B 564 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7849 (tp40) REVERT: B 661 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 994 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (t0) REVERT: C 153 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.5947 (pmm) REVERT: C 309 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: C 495 TYR cc_start: 0.7216 (t80) cc_final: 0.6597 (t80) REVERT: C 868 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: C 994 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (t0) REVERT: C 1092 GLU cc_start: 0.8363 (tp30) cc_final: 0.7494 (pt0) REVERT: C 1144 GLU cc_start: 0.8563 (mp0) cc_final: 0.8180 (mp0) REVERT: H 39 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8002 (tp) REVERT: H 45 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8089 (mmt90) REVERT: H 53 ILE cc_start: 0.6625 (mm) cc_final: 0.6183 (mp) REVERT: L 27 GLN cc_start: 0.7995 (mp10) cc_final: 0.7556 (mp10) REVERT: L 42 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: L 66 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: M 21 MET cc_start: 0.5800 (mmt) cc_final: 0.5480 (mpt) REVERT: M 43 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6638 (ttmm) REVERT: M 113 ARG cc_start: 0.7635 (mpp-170) cc_final: 0.6858 (ptp-110) REVERT: N 27 GLN cc_start: 0.8082 (mp-120) cc_final: 0.7838 (mp10) REVERT: P 43 LYS cc_start: 0.7055 (tttt) cc_final: 0.6540 (tmtt) REVERT: P 89 MET cc_start: 0.3911 (ppp) cc_final: 0.3385 (ppp) REVERT: P 108 ASP cc_start: 0.7154 (t70) cc_final: 0.6922 (t70) REVERT: P 113 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7762 (mtm110) outliers start: 86 outliers final: 50 residues processed: 328 average time/residue: 0.5101 time to fit residues: 206.9323 Evaluate side-chains 335 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 42 TYR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 76 optimal weight: 2.9990 chunk 231 optimal weight: 0.0670 chunk 281 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.198556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129211 restraints weight = 38792.478| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.07 r_work: 0.3287 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31767 Z= 0.165 Angle : 0.591 12.035 43383 Z= 0.292 Chirality : 0.046 0.329 4971 Planarity : 0.004 0.057 5544 Dihedral : 4.290 28.165 4197 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 2.47 % Allowed : 14.60 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3864 helix: 2.24 (0.20), residues: 657 sheet: -0.36 (0.16), residues: 1045 loop : -0.88 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 45 TYR 0.030 0.001 TYR A 170 PHE 0.016 0.001 PHE A 898 TRP 0.016 0.001 TRP P 38 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (31686) covalent geometry : angle 0.56331 / 0.29 (43182) SS BOND : bond 0.00440 / 0.25 ( 42) SS BOND : angle 0.90670 / 0.65 ( 84) hydrogen bonds : bond 0.03897 / 2.63 ( 1131) hydrogen bonds : angle 5.74049 / 3.93 ( 3171) link_NAG-ASN : bond 0.00727 / 0.46 ( 39) link_NAG-ASN : angle 3.43439 / 2.45 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.4966 (mmt180) cc_final: 0.4737 (mmt180) REVERT: A 129 LYS cc_start: 0.6947 (tmtt) cc_final: 0.6501 (tptp) REVERT: A 153 MET cc_start: 0.6999 (tpt) cc_final: 0.6579 (ptt) REVERT: A 177 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.4869 (ppp) REVERT: A 233 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5519 (mt) REVERT: A 273 ARG cc_start: 0.5896 (mtt-85) cc_final: 0.5477 (mmm-85) REVERT: A 357 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7723 (ptm160) REVERT: A 467 ASP cc_start: 0.7541 (t70) cc_final: 0.7102 (t0) REVERT: A 558 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8327 (mptp) REVERT: A 574 ASP cc_start: 0.7829 (t0) cc_final: 0.7484 (t0) REVERT: A 756 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: A 1092 GLU cc_start: 0.8316 (tp30) cc_final: 0.7253 (pt0) REVERT: B 170 TYR cc_start: 0.5644 (t80) cc_final: 0.5259 (t80) REVERT: B 237 ARG cc_start: 0.6638 (mtm-85) cc_final: 0.6285 (mpp80) REVERT: B 564 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7988 (tp40) REVERT: B 994 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 153 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.5987 (pmm) REVERT: C 309 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: C 495 TYR cc_start: 0.7239 (t80) cc_final: 0.6592 (t80) REVERT: C 675 GLN cc_start: 0.7777 (mt0) cc_final: 0.6767 (pp30) REVERT: C 868 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: C 994 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8101 (t0) REVERT: C 1092 GLU cc_start: 0.8368 (tp30) cc_final: 0.7501 (pt0) REVERT: C 1144 GLU cc_start: 0.8567 (mp0) cc_final: 0.8178 (mp0) REVERT: H 43 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7207 (ttmm) REVERT: H 45 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8171 (mmt90) REVERT: H 53 ILE cc_start: 0.6705 (mm) cc_final: 0.6299 (mt) REVERT: L 27 GLN cc_start: 0.8033 (mp10) cc_final: 0.7544 (mp10) REVERT: L 66 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7825 (mt-10) REVERT: M 21 MET cc_start: 0.5794 (mmt) cc_final: 0.5505 (mpt) REVERT: M 43 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6648 (ttmm) REVERT: M 45 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8598 (mtp-110) REVERT: M 64 PHE cc_start: 0.8163 (t80) cc_final: 0.7496 (t80) REVERT: M 113 ARG cc_start: 0.7635 (mpp-170) cc_final: 0.6877 (ptp-110) REVERT: N 27 GLN cc_start: 0.8111 (mp-120) cc_final: 0.7880 (mp10) REVERT: P 89 MET cc_start: 0.3957 (ppp) cc_final: 0.3424 (ppp) REVERT: P 108 ASP cc_start: 0.7146 (t70) cc_final: 0.6881 (t70) outliers start: 83 outliers final: 50 residues processed: 332 average time/residue: 0.5238 time to fit residues: 213.1556 Evaluate side-chains 328 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 363 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.200070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123242 restraints weight = 38613.101| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.64 r_work: 0.3378 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31767 Z= 0.118 Angle : 0.567 12.061 43383 Z= 0.281 Chirality : 0.045 0.326 4971 Planarity : 0.004 0.059 5544 Dihedral : 4.191 27.047 4197 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 15.07 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.23 (0.13), residues: 3864 helix: 2.40 (0.20), residues: 656 sheet: -0.35 (0.16), residues: 1053 loop : -0.85 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 346 TYR 0.024 0.001 TYR L 42 PHE 0.017 0.001 PHE A 898 TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (31686) covalent geometry : angle 0.53941 / 0.28 (43182) SS BOND : bond 0.00271 / 0.16 ( 42) SS BOND : angle 0.79393 / 0.57 ( 84) hydrogen bonds : bond 0.03573 / 2.40 ( 1131) hydrogen bonds : angle 5.59669 / 3.83 ( 3171) link_NAG-ASN : bond 0.00732 / 0.46 ( 39) link_NAG-ASN : angle 3.35002 / 2.40 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 268 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.6861 (m-80) cc_final: 0.6235 (m-80) REVERT: A 153 MET cc_start: 0.7003 (tpt) cc_final: 0.6634 (ptt) REVERT: A 177 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.4756 (ppp) REVERT: A 233 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5530 (mt) REVERT: A 273 ARG cc_start: 0.5757 (mtt-85) cc_final: 0.5369 (mmm-85) REVERT: A 357 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7700 (ptm160) REVERT: A 467 ASP cc_start: 0.7485 (t70) cc_final: 0.7056 (t0) REVERT: A 495 TYR cc_start: 0.6641 (t80) cc_final: 0.6425 (t80) REVERT: A 558 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8294 (mptp) REVERT: A 574 ASP cc_start: 0.7810 (t0) cc_final: 0.7566 (t0) REVERT: A 756 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: A 868 GLU cc_start: 0.7992 (tt0) cc_final: 0.7241 (tp30) REVERT: A 1092 GLU cc_start: 0.8281 (tp30) cc_final: 0.7299 (pt0) REVERT: B 170 TYR cc_start: 0.5516 (t80) cc_final: 0.5116 (t80) REVERT: B 237 ARG cc_start: 0.6536 (mtm-85) cc_final: 0.6189 (mpp80) REVERT: B 564 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8003 (tp40) REVERT: B 661 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 994 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8005 (t0) REVERT: C 153 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.5899 (pmm) REVERT: C 177 MET cc_start: 0.5947 (mtt) cc_final: 0.5522 (mpp) REVERT: C 495 TYR cc_start: 0.7178 (t80) cc_final: 0.6559 (t80) REVERT: C 868 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: C 994 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7975 (t0) REVERT: C 1092 GLU cc_start: 0.8267 (tp30) cc_final: 0.7486 (pt0) REVERT: C 1094 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7429 (p) REVERT: C 1144 GLU cc_start: 0.8560 (mp0) cc_final: 0.8174 (mp0) REVERT: H 39 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7609 (mm) REVERT: H 53 ILE cc_start: 0.6487 (mm) cc_final: 0.6097 (mt) REVERT: L 27 GLN cc_start: 0.8037 (mp10) cc_final: 0.7539 (mp10) REVERT: L 66 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7799 (mt-10) REVERT: M 21 MET cc_start: 0.5761 (mmt) cc_final: 0.5425 (mpt) REVERT: M 43 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6512 (ttmm) REVERT: M 45 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8563 (mtp-110) REVERT: M 64 PHE cc_start: 0.8127 (t80) cc_final: 0.7536 (t80) REVERT: M 113 ARG cc_start: 0.7575 (mpp-170) cc_final: 0.6814 (ptp-110) REVERT: N 27 GLN cc_start: 0.8124 (mp-120) cc_final: 0.7834 (mp10) REVERT: N 39 ILE cc_start: 0.7534 (mm) cc_final: 0.6981 (tt) REVERT: P 43 LYS cc_start: 0.6977 (tttt) cc_final: 0.6494 (tmtt) REVERT: P 89 MET cc_start: 0.3996 (ppp) cc_final: 0.3448 (ppp) REVERT: P 108 ASP cc_start: 0.7126 (t70) cc_final: 0.6753 (t70) REVERT: P 113 ARG cc_start: 0.7745 (mtm110) cc_final: 0.6705 (ptp-110) outliers start: 70 outliers final: 42 residues processed: 313 average time/residue: 0.5084 time to fit residues: 196.1893 Evaluate side-chains 312 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 66 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 302 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 787 GLN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117620 restraints weight = 38108.810| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.63 r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31767 Z= 0.198 Angle : 0.613 12.485 43383 Z= 0.304 Chirality : 0.047 0.332 4971 Planarity : 0.004 0.058 5544 Dihedral : 4.307 27.227 4197 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 1.85 % Allowed : 15.40 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.30 (0.13), residues: 3864 helix: 2.21 (0.20), residues: 657 sheet: -0.34 (0.16), residues: 1051 loop : -0.89 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 75 TYR 0.024 0.002 TYR A 170 PHE 0.020 0.001 PHE M 71 TRP 0.013 0.001 TRP H 52 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (31686) covalent geometry : angle 0.58602 / 0.30 (43182) SS BOND : bond 0.00567 / 0.32 ( 42) SS BOND : angle 0.94514 / 0.68 ( 84) hydrogen bonds : bond 0.04062 / 2.74 ( 1131) hydrogen bonds : angle 5.72655 / 3.92 ( 3171) link_NAG-ASN : bond 0.00724 / 0.45 ( 39) link_NAG-ASN : angle 3.44559 / 2.46 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 269 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6883 (tmtt) cc_final: 0.6327 (tptp) REVERT: A 153 MET cc_start: 0.6990 (tpt) cc_final: 0.6624 (ptt) REVERT: A 177 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.4791 (ppp) REVERT: A 273 ARG cc_start: 0.5695 (mtt-85) cc_final: 0.5295 (mmm-85) REVERT: A 357 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7647 (ptm160) REVERT: A 467 ASP cc_start: 0.7520 (t70) cc_final: 0.7098 (t0) REVERT: A 495 TYR cc_start: 0.6710 (t80) cc_final: 0.6463 (t80) REVERT: A 558 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8274 (mptp) REVERT: A 574 ASP cc_start: 0.7761 (t0) cc_final: 0.7344 (t0) REVERT: A 675 GLN cc_start: 0.7592 (mt0) cc_final: 0.6671 (pp30) REVERT: A 756 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: A 868 GLU cc_start: 0.7940 (tt0) cc_final: 0.7121 (tp30) REVERT: A 1092 GLU cc_start: 0.8262 (tp30) cc_final: 0.7185 (pt0) REVERT: B 153 MET cc_start: 0.7117 (mmm) cc_final: 0.6843 (mmm) REVERT: B 168 PHE cc_start: 0.3299 (t80) cc_final: 0.3089 (t80) REVERT: B 170 TYR cc_start: 0.5541 (t80) cc_final: 0.5115 (t80) REVERT: B 237 ARG cc_start: 0.6480 (mtm-85) cc_final: 0.6279 (mtm-85) REVERT: B 564 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7716 (tp40) REVERT: B 661 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 675 GLN cc_start: 0.7444 (mt0) cc_final: 0.6461 (pp30) REVERT: C 153 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.5991 (pmm) REVERT: C 177 MET cc_start: 0.6032 (mtt) cc_final: 0.5596 (mpp) REVERT: C 495 TYR cc_start: 0.7208 (t80) cc_final: 0.6570 (t80) REVERT: C 675 GLN cc_start: 0.7685 (mt0) cc_final: 0.6665 (pp30) REVERT: C 1092 GLU cc_start: 0.8338 (tp30) cc_final: 0.7437 (pt0) REVERT: C 1144 GLU cc_start: 0.8522 (mp0) cc_final: 0.8121 (mp0) REVERT: H 21 MET cc_start: 0.4925 (mmm) cc_final: 0.3982 (mmt) REVERT: H 53 ILE cc_start: 0.6425 (mm) cc_final: 0.5997 (mt) REVERT: L 27 GLN cc_start: 0.7982 (mp10) cc_final: 0.7465 (mp10) REVERT: L 66 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: M 21 MET cc_start: 0.5742 (mmt) cc_final: 0.5436 (mpt) REVERT: M 45 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8538 (mtp-110) REVERT: M 64 PHE cc_start: 0.8154 (t80) cc_final: 0.7522 (t80) REVERT: M 113 ARG cc_start: 0.7555 (mpp-170) cc_final: 0.6820 (ptp-110) REVERT: N 27 GLN cc_start: 0.8068 (mp-120) cc_final: 0.7800 (mp10) REVERT: N 39 ILE cc_start: 0.7525 (mm) cc_final: 0.6988 (tt) REVERT: P 89 MET cc_start: 0.3895 (ppp) cc_final: 0.3390 (ppp) REVERT: P 108 ASP cc_start: 0.7227 (t70) cc_final: 0.6774 (t70) REVERT: P 113 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7465 (ptp-110) outliers start: 62 outliers final: 41 residues processed: 307 average time/residue: 0.5255 time to fit residues: 199.7087 Evaluate side-chains 311 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 185 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 297 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.196812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119492 restraints weight = 38430.389| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.63 r_work: 0.3334 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31767 Z= 0.137 Angle : 0.585 12.035 43383 Z= 0.288 Chirality : 0.046 0.326 4971 Planarity : 0.004 0.059 5544 Dihedral : 4.220 26.429 4197 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 1.73 % Allowed : 15.64 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.23 (0.13), residues: 3864 helix: 2.44 (0.20), residues: 644 sheet: -0.37 (0.16), residues: 1033 loop : -0.84 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 75 TYR 0.023 0.001 TYR C 453 PHE 0.032 0.001 PHE P 64 TRP 0.013 0.001 TRP H 52 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (31686) covalent geometry : angle 0.55815 / 0.28 (43182) SS BOND : bond 0.00354 / 0.20 ( 42) SS BOND : angle 0.80936 / 0.59 ( 84) hydrogen bonds : bond 0.03684 / 2.48 ( 1131) hydrogen bonds : angle 5.61129 / 3.83 ( 3171) link_NAG-ASN : bond 0.00733 / 0.46 ( 39) link_NAG-ASN : angle 3.37408 / 2.41 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13299.73 seconds wall clock time: 226 minutes 39.63 seconds (13599.63 seconds total)