Starting phenix.real_space_refine on Sun Jul 5 05:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xus_38682/07_2026/8xus_38682.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.085 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 115 5.16 5 C 16395 2.51 5 N 4203 2.21 5 O 5000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 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: 25713 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 267 Unusual residues: {'IDU': 1, 'NAG': 18} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 20 Time building chain proxies: 5.50, per 1000 atoms: 0.21 Number of scatterers: 25713 At special positions: 0 Unit cell: (149.184, 146.076, 171.976, 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 115 16.00 O 5000 8.00 N 4203 7.00 C 16395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 245 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 354 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG A1317 " - " ASN A 61 " " NAG A1318 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 245 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 354 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B 801 " " NAG B1314 " - " ASN B1074 " " NAG B1315 " - " ASN B1098 " " NAG B1316 " - " ASN B1134 " " NAG B1318 " - " ASN B 603 " " NAG B1319 " - " ASN B 61 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 245 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 354 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C 801 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C1098 " " NAG C1316 " - " ASN C1134 " " NAG C1317 " - " ASN C 61 " " NAG C1318 " - " ASN C 603 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 45 sheets defined 26.0% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.728A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.557A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.874A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.574A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.848A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.400A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.582A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.728A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.278A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.574A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.418A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.582A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.728A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.328A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.574A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.514A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.344A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.564A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.256A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.626A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.777A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.403A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.321A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.602A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.313A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.648A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.185A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 788 removed outlier: 3.560A pdb=" N ILE C 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.256A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.527A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.777A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 120 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.077A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.716A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.340A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 539 through 543 removed outlier: 4.427A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.314A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.632A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.185A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 26 through 29 removed outlier: 7.204A pdb=" N THR B 63 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR B 266 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 65 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP B 264 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.624A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.777A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.403A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.715A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.325A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.313A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.610A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.184A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1081 through 1082 932 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4773 1.33 - 1.45: 6910 1.45 - 1.57: 14488 1.57 - 1.69: 1 1.69 - 1.81: 141 Bond restraints: 26313 Sorted by residual: bond pdb=" CA GLN B 564 " pdb=" C GLN B 564 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.63e+01 bond pdb=" CA GLN A 564 " pdb=" C GLN A 564 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.51e+01 bond pdb=" CA GLN C 564 " pdb=" C GLN C 564 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.49e+01 bond pdb=" N VAL B1128 " pdb=" CA VAL B1128 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.59e+01 bond pdb=" N VAL A1128 " pdb=" CA VAL A1128 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.57e+01 ... (remaining 26308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 32902 2.12 - 4.24: 2565 4.24 - 6.35: 257 6.35 - 8.47: 78 8.47 - 10.59: 10 Bond angle restraints: 35812 Sorted by residual: angle pdb=" N GLU B 988 " pdb=" CA GLU B 988 " pdb=" C GLU B 988 " ideal model delta sigma weight residual 113.43 105.30 8.13 1.26e+00 6.30e-01 4.16e+01 angle pdb=" O THR C 323 " pdb=" C THR C 323 " pdb=" N GLU C 324 " ideal model delta sigma weight residual 122.32 129.40 -7.08 1.15e+00 7.56e-01 3.79e+01 angle pdb=" O THR B 323 " pdb=" C THR B 323 " pdb=" N GLU B 324 " ideal model delta sigma weight residual 122.32 129.38 -7.06 1.15e+00 7.56e-01 3.77e+01 angle pdb=" O THR A 323 " pdb=" C THR A 323 " pdb=" N GLU A 324 " ideal model delta sigma weight residual 122.32 129.38 -7.06 1.15e+00 7.56e-01 3.77e+01 angle pdb=" CA THR B 323 " pdb=" C THR B 323 " pdb=" N GLU B 324 " ideal model delta sigma weight residual 117.07 109.85 7.22 1.21e+00 6.83e-01 3.56e+01 ... (remaining 35807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.58: 14940 23.58 - 47.15: 1224 47.15 - 70.73: 169 70.73 - 94.31: 24 94.31 - 117.88: 3 Dihedral angle restraints: 16360 sinusoidal: 7084 harmonic: 9276 Sorted by residual: dihedral pdb=" CD ARG B 328 " pdb=" NE ARG B 328 " pdb=" CZ ARG B 328 " pdb=" NH1 ARG B 328 " ideal model delta sinusoidal sigma weight residual 0.00 -88.71 88.71 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CD ARG A 328 " pdb=" NE ARG A 328 " pdb=" CZ ARG A 328 " pdb=" NH1 ARG A 328 " ideal model delta sinusoidal sigma weight residual 0.00 -88.66 88.66 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CD ARG C 328 " pdb=" NE ARG C 328 " pdb=" CZ ARG C 328 " pdb=" NH1 ARG C 328 " ideal model delta sinusoidal sigma weight residual 0.00 -88.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 ... (remaining 16357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3573 0.104 - 0.209: 559 0.209 - 0.313: 51 0.313 - 0.417: 10 0.417 - 0.522: 1 Chirality restraints: 4194 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CB VAL B1096 " pdb=" CA VAL B1096 " pdb=" CG1 VAL B1096 " pdb=" CG2 VAL B1096 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB VAL A1096 " pdb=" CA VAL A1096 " pdb=" CG1 VAL A1096 " pdb=" CG2 VAL A1096 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 4191 not shown) Planarity restraints: 4618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 328 " 1.109 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG B 328 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 328 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 328 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 328 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 328 " -1.109 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG C 328 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 328 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 328 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 328 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " 1.108 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG A 328 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " 0.017 2.00e-02 2.50e+03 ... (remaining 4615 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 109 2.46 - 3.07: 18321 3.07 - 3.68: 38931 3.68 - 4.29: 57222 4.29 - 4.90: 93976 Nonbonded interactions: 208559 Sorted by model distance: nonbonded pdb=" O3 IDU B1317 " pdb=" O3S IDU B1317 " model vdw 1.847 3.040 nonbonded pdb=" O ASN C 417 " pdb=" ND2 ASN C 422 " model vdw 2.196 3.120 nonbonded pdb=" CG2 VAL C 503 " pdb=" CE1 HIS A 505 " model vdw 2.199 3.680 nonbonded pdb=" CG2 VAL A 503 " pdb=" CE1 HIS B 505 " model vdw 2.211 3.680 nonbonded pdb=" O GLN A 965 " pdb=" OG SER A 968 " model vdw 2.215 3.040 ... (remaining 208554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 1316 or resid 1318)) selection = (chain 'B' and (resid 23 through 1316 or resid 1318)) selection = (chain 'C' and (resid 23 through 1316 or resid 1318)) } 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: 2.210 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.720 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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 : 0.008 0.077 26406 Z= 0.584 Angle : 1.195 10.649 36052 Z= 0.787 Chirality : 0.075 0.522 4194 Planarity : 0.017 0.497 4564 Dihedral : 15.790 117.885 10285 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 1.74 % Allowed : 8.67 % Favored : 89.59 % Rotamer: Outliers : 3.57 % Allowed : 19.57 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 3159 helix: 0.54 (0.20), residues: 732 sheet: -1.49 (0.19), residues: 699 loop : -2.60 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 328 TYR 0.019 0.002 TYR A 904 PHE 0.022 0.002 PHE B 338 TRP 0.011 0.002 TRP A1102 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.58 (26313) covalent geometry : angle 1.17090 / 0.78 (35812) SS BOND : bond 0.00493 / 0.33 ( 39) SS BOND : angle 1.36807 / 0.86 ( 78) hydrogen bonds : bond 0.20391 / 13.27 ( 932) hydrogen bonds : angle 8.84885 / 6.05 ( 2553) link_NAG-ASN : bond 0.00854 / 0.46 ( 54) link_NAG-ASN : angle 3.75272 / 2.42 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 769 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 THR cc_start: 0.8485 (m) cc_final: 0.8275 (t) REVERT: C 278 LYS cc_start: 0.7402 (tmtt) cc_final: 0.7007 (ttpt) REVERT: C 382 VAL cc_start: 0.6243 (t) cc_final: 0.5674 (t) REVERT: C 425 LEU cc_start: 0.8538 (mt) cc_final: 0.8315 (mt) REVERT: C 508 TYR cc_start: 0.6708 (m-80) cc_final: 0.6358 (m-10) REVERT: C 521 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: C 590 CYS cc_start: 0.7104 (m) cc_final: 0.6754 (m) REVERT: C 592 PHE cc_start: 0.6480 (t80) cc_final: 0.6114 (t80) REVERT: C 1102 TRP cc_start: 0.7868 (m100) cc_final: 0.6632 (m100) REVERT: A 33 THR cc_start: 0.8557 (m) cc_final: 0.8079 (p) REVERT: A 41 LYS cc_start: 0.7122 (mttp) cc_final: 0.6613 (mtpp) REVERT: A 46 SER cc_start: 0.8477 (m) cc_final: 0.7812 (t) REVERT: A 113 LYS cc_start: 0.7144 (tptt) cc_final: 0.6897 (tttm) REVERT: A 298 GLU cc_start: 0.7338 (tt0) cc_final: 0.7131 (mt-10) REVERT: A 360 ASN cc_start: 0.7585 (m-40) cc_final: 0.7119 (t0) REVERT: A 389 ASP cc_start: 0.7513 (m-30) cc_final: 0.6420 (t0) REVERT: A 400 PHE cc_start: 0.7412 (p90) cc_final: 0.7084 (p90) REVERT: A 558 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6712 (mmtp) REVERT: A 564 GLN cc_start: 0.6466 (mm-40) cc_final: 0.6234 (mm110) REVERT: A 590 CYS cc_start: 0.7201 (m) cc_final: 0.6791 (m) REVERT: A 697 MET cc_start: 0.7140 (ptm) cc_final: 0.6897 (ptp) REVERT: A 752 LEU cc_start: 0.7852 (mt) cc_final: 0.7422 (mp) REVERT: A 868 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6414 (mp0) REVERT: A 933 LYS cc_start: 0.7826 (ptpt) cc_final: 0.7264 (mttp) REVERT: A 998 THR cc_start: 0.8815 (m) cc_final: 0.8556 (m) REVERT: A 1005 GLN cc_start: 0.7487 (tp40) cc_final: 0.7189 (mt0) REVERT: A 1125 ASN cc_start: 0.7252 (t0) cc_final: 0.6406 (t0) REVERT: B 202 LYS cc_start: 0.7354 (mttm) cc_final: 0.7074 (mptt) REVERT: B 286 THR cc_start: 0.8016 (m) cc_final: 0.7705 (p) REVERT: B 287 ASP cc_start: 0.6510 (m-30) cc_final: 0.5304 (m-30) REVERT: B 298 GLU cc_start: 0.7219 (tt0) cc_final: 0.6649 (tt0) REVERT: B 327 VAL cc_start: 0.7911 (t) cc_final: 0.7500 (p) REVERT: B 1096 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7788 (m) outliers start: 99 outliers final: 19 residues processed: 832 average time/residue: 0.1806 time to fit residues: 237.7883 Evaluate side-chains 420 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 400 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 919 ASN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS A 164 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 784 GLN A1101 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 762 GLN B 804 GLN B 895 GLN B 913 GLN B 919 ASN B 935 GLN B 992 GLN B1071 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.203492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170921 restraints weight = 36304.454| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.31 r_work: 0.3880 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26406 Z= 0.176 Angle : 0.816 19.636 36052 Z= 0.399 Chirality : 0.053 0.612 4194 Planarity : 0.006 0.048 4564 Dihedral : 6.602 58.166 4610 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.38 % Favored : 92.12 % Rotamer: Outliers : 4.61 % Allowed : 19.28 % Favored : 76.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3159 helix: 1.38 (0.20), residues: 708 sheet: -0.99 (0.19), residues: 696 loop : -2.31 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.020 0.002 TYR A1067 PHE 0.025 0.002 PHE B 338 TRP 0.012 0.002 TRP A 64 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (26313) covalent geometry : angle 0.76327 / 0.39 (35812) SS BOND : bond 0.00417 / 0.23 ( 39) SS BOND : angle 1.40441 / 0.76 ( 78) hydrogen bonds : bond 0.04642 / 3.01 ( 932) hydrogen bonds : angle 6.42336 / 4.39 ( 2553) link_NAG-ASN : bond 0.00909 / 0.45 ( 54) link_NAG-ASN : angle 4.27951 / 2.74 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 422 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 434 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7552 (mt) REVERT: C 508 TYR cc_start: 0.6398 (m-80) cc_final: 0.6099 (m-10) REVERT: C 1102 TRP cc_start: 0.8108 (m100) cc_final: 0.7002 (m100) REVERT: A 33 THR cc_start: 0.8453 (m) cc_final: 0.8102 (p) REVERT: A 46 SER cc_start: 0.8452 (m) cc_final: 0.7972 (t) REVERT: A 113 LYS cc_start: 0.7184 (tptt) cc_final: 0.6798 (tppt) REVERT: A 127 PHE cc_start: 0.7475 (t80) cc_final: 0.7178 (t80) REVERT: A 133 PHE cc_start: 0.6941 (m-80) cc_final: 0.6517 (m-80) REVERT: A 177 MET cc_start: 0.3595 (mmt) cc_final: 0.3318 (mmp) REVERT: A 200 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5410 (t80) REVERT: A 360 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7558 (t0) REVERT: A 389 ASP cc_start: 0.7920 (m-30) cc_final: 0.6702 (t0) REVERT: A 457 ARG cc_start: 0.5789 (ttt-90) cc_final: 0.5584 (ttt-90) REVERT: A 558 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7656 (mmtt) REVERT: A 590 CYS cc_start: 0.7400 (m) cc_final: 0.7048 (m) REVERT: A 619 GLU cc_start: 0.8116 (tp30) cc_final: 0.7771 (mp0) REVERT: A 697 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (ptp) REVERT: A 752 LEU cc_start: 0.8401 (mt) cc_final: 0.8143 (mp) REVERT: A 1005 GLN cc_start: 0.8299 (tp40) cc_final: 0.8060 (mt0) REVERT: A 1017 GLU cc_start: 0.8539 (tp30) cc_final: 0.8193 (tt0) REVERT: A 1019 ARG cc_start: 0.8529 (tpt170) cc_final: 0.8004 (ttp80) REVERT: A 1125 ASN cc_start: 0.7499 (t0) cc_final: 0.6730 (t0) REVERT: B 28 TYR cc_start: 0.6354 (m-10) cc_final: 0.5850 (m-10) REVERT: B 127 PHE cc_start: 0.6364 (t80) cc_final: 0.6158 (t80) REVERT: B 129 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6073 (mttt) REVERT: B 202 LYS cc_start: 0.8195 (mttm) cc_final: 0.7930 (mmtp) REVERT: B 278 LYS cc_start: 0.8653 (tttt) cc_final: 0.8198 (ttpt) REVERT: B 346 ARG cc_start: 0.7355 (ptp-170) cc_final: 0.6083 (mmm-85) REVERT: B 556 ASN cc_start: 0.5448 (m110) cc_final: 0.5222 (t0) REVERT: B 663 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8225 (t0) REVERT: B 916 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6777 (tp) REVERT: B 1091 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.7034 (mtt-85) outliers start: 128 outliers final: 61 residues processed: 518 average time/residue: 0.1537 time to fit residues: 131.9866 Evaluate side-chains 397 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 329 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 50 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 116 optimal weight: 30.0000 chunk 170 optimal weight: 0.0070 chunk 164 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 957 GLN A 99 ASN A 207 HIS A 540 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 856 ASN B 965 GLN B1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.202192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171088 restraints weight = 36277.683| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.06 r_work: 0.3868 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26406 Z= 0.130 Angle : 0.705 22.358 36052 Z= 0.343 Chirality : 0.047 0.483 4194 Planarity : 0.005 0.061 4564 Dihedral : 5.901 53.631 4585 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.12 % Favored : 92.53 % Rotamer: Outliers : 4.40 % Allowed : 19.71 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3159 helix: 1.56 (0.19), residues: 708 sheet: -1.03 (0.19), residues: 687 loop : -2.08 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.019 0.001 TYR A 313 PHE 0.021 0.001 PHE A 338 TRP 0.019 0.001 TRP A 353 HIS 0.005 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26313) covalent geometry : angle 0.64307 / 0.33 (35812) SS BOND : bond 0.00257 / 0.14 ( 39) SS BOND : angle 1.10806 / 0.57 ( 78) hydrogen bonds : bond 0.04015 / 2.63 ( 932) hydrogen bonds : angle 5.94065 / 4.06 ( 2553) link_NAG-ASN : bond 0.00659 / 0.37 ( 54) link_NAG-ASN : angle 4.29523 / 2.87 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 374 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.6005 (OUTLIER) cc_final: 0.5796 (tp40) REVERT: C 353 TRP cc_start: 0.7883 (p-90) cc_final: 0.7671 (p-90) REVERT: C 423 TYR cc_start: 0.7953 (t80) cc_final: 0.7752 (t80) REVERT: C 508 TYR cc_start: 0.6413 (m-80) cc_final: 0.6162 (m-10) REVERT: C 900 MET cc_start: 0.6963 (mmm) cc_final: 0.6712 (mtt) REVERT: C 936 ASP cc_start: 0.7705 (m-30) cc_final: 0.7474 (m-30) REVERT: A 33 THR cc_start: 0.8332 (m) cc_final: 0.7997 (p) REVERT: A 46 SER cc_start: 0.8433 (m) cc_final: 0.7956 (t) REVERT: A 113 LYS cc_start: 0.7230 (tptt) cc_final: 0.6868 (tppt) REVERT: A 127 PHE cc_start: 0.7050 (t80) cc_final: 0.6818 (t80) REVERT: A 133 PHE cc_start: 0.6917 (m-80) cc_final: 0.6676 (m-80) REVERT: A 200 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5405 (t80) REVERT: A 353 TRP cc_start: 0.7968 (p-90) cc_final: 0.7659 (p-90) REVERT: A 360 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7542 (t0) REVERT: A 389 ASP cc_start: 0.7867 (m-30) cc_final: 0.6797 (t0) REVERT: A 434 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6383 (mp) REVERT: A 558 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7883 (mmtt) REVERT: A 590 CYS cc_start: 0.7498 (m) cc_final: 0.7255 (m) REVERT: A 619 GLU cc_start: 0.8217 (tp30) cc_final: 0.7924 (mt-10) REVERT: A 697 MET cc_start: 0.7462 (ptm) cc_final: 0.7065 (ttp) REVERT: A 1017 GLU cc_start: 0.8492 (tp30) cc_final: 0.8181 (tt0) REVERT: A 1019 ARG cc_start: 0.8466 (tpt170) cc_final: 0.8084 (ttp80) REVERT: A 1125 ASN cc_start: 0.7327 (t0) cc_final: 0.6644 (t0) REVERT: B 28 TYR cc_start: 0.6458 (m-10) cc_final: 0.6224 (m-10) REVERT: B 130 VAL cc_start: 0.8046 (t) cc_final: 0.7635 (t) REVERT: B 278 LYS cc_start: 0.8701 (tttt) cc_final: 0.8391 (ttpt) REVERT: B 556 ASN cc_start: 0.5670 (m110) cc_final: 0.5464 (t0) REVERT: B 663 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 1132 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6602 (tp) outliers start: 122 outliers final: 77 residues processed: 459 average time/residue: 0.1428 time to fit residues: 108.3601 Evaluate side-chains 410 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 93 optimal weight: 0.7980 chunk 291 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS A 564 GLN A 613 GLN A1002 GLN A1005 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 856 ASN B1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159778 restraints weight = 35830.061| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.18 r_work: 0.3740 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26406 Z= 0.182 Angle : 0.719 17.113 36052 Z= 0.356 Chirality : 0.050 0.667 4194 Planarity : 0.005 0.068 4564 Dihedral : 5.888 58.924 4585 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.21 % Rotamer: Outliers : 4.65 % Allowed : 21.15 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3159 helix: 1.57 (0.19), residues: 705 sheet: -0.98 (0.19), residues: 711 loop : -2.04 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.016 0.002 TYR B 160 PHE 0.024 0.002 PHE A 898 TRP 0.034 0.002 TRP C 633 HIS 0.005 0.001 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (26313) covalent geometry : angle 0.66813 / 0.34 (35812) SS BOND : bond 0.00429 / 0.23 ( 39) SS BOND : angle 1.48180 / 0.75 ( 78) hydrogen bonds : bond 0.04307 / 2.79 ( 932) hydrogen bonds : angle 5.73245 / 3.90 ( 2553) link_NAG-ASN : bond 0.01107 / 0.62 ( 54) link_NAG-ASN : angle 3.91292 / 2.65 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 361 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.7539 (pt) cc_final: 0.7113 (tt) REVERT: C 452 TRP cc_start: 0.7843 (m100) cc_final: 0.7551 (m100) REVERT: C 508 TYR cc_start: 0.6571 (m-80) cc_final: 0.6275 (m-10) REVERT: C 751 ASN cc_start: 0.7708 (m-40) cc_final: 0.7488 (m110) REVERT: C 998 THR cc_start: 0.9020 (m) cc_final: 0.8801 (p) REVERT: A 33 THR cc_start: 0.8459 (m) cc_final: 0.8168 (p) REVERT: A 46 SER cc_start: 0.8606 (m) cc_final: 0.8109 (t) REVERT: A 113 LYS cc_start: 0.7238 (tptt) cc_final: 0.6963 (tppt) REVERT: A 200 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5033 (t80) REVERT: A 360 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7587 (t0) REVERT: A 389 ASP cc_start: 0.7833 (m-30) cc_final: 0.6863 (t0) REVERT: A 434 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6460 (mp) REVERT: A 558 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8032 (mmtt) REVERT: A 590 CYS cc_start: 0.7520 (m) cc_final: 0.7226 (m) REVERT: A 619 GLU cc_start: 0.8278 (tp30) cc_final: 0.8040 (mt-10) REVERT: A 759 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 779 GLN cc_start: 0.7894 (tp40) cc_final: 0.7411 (tt0) REVERT: A 902 MET cc_start: 0.7983 (mmm) cc_final: 0.7705 (tpt) REVERT: A 1017 GLU cc_start: 0.8469 (tp30) cc_final: 0.8136 (tt0) REVERT: A 1019 ARG cc_start: 0.8607 (tpt170) cc_final: 0.8208 (ttp80) REVERT: A 1125 ASN cc_start: 0.7375 (t0) cc_final: 0.6547 (t0) REVERT: B 127 PHE cc_start: 0.6441 (t80) cc_final: 0.6202 (t80) REVERT: B 129 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6372 (mttt) REVERT: B 278 LYS cc_start: 0.8844 (tttt) cc_final: 0.8547 (ttpt) REVERT: B 346 ARG cc_start: 0.7463 (ptp-170) cc_final: 0.6227 (mmm-85) REVERT: B 349 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6818 (m) REVERT: B 556 ASN cc_start: 0.6078 (m110) cc_final: 0.5781 (t0) REVERT: B 569 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6881 (tp) REVERT: B 663 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8287 (t0) REVERT: B 773 GLU cc_start: 0.6796 (tt0) cc_final: 0.6517 (tt0) REVERT: B 860 VAL cc_start: 0.8886 (t) cc_final: 0.8637 (t) outliers start: 129 outliers final: 78 residues processed: 454 average time/residue: 0.1487 time to fit residues: 111.2367 Evaluate side-chains 399 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 313 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 258 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 243 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN A 134 GLN A 505 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1083 HIS B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 856 ASN B 935 GLN B1002 GLN B1005 GLN B1036 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.190011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156502 restraints weight = 35751.930| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.07 r_work: 0.3717 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26406 Z= 0.189 Angle : 0.732 16.477 36052 Z= 0.357 Chirality : 0.048 0.465 4194 Planarity : 0.005 0.062 4564 Dihedral : 5.867 56.019 4582 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.28 % Favored : 92.50 % Rotamer: Outliers : 5.23 % Allowed : 21.41 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3159 helix: 1.53 (0.19), residues: 705 sheet: -1.12 (0.19), residues: 714 loop : -1.95 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.002 TYR A 421 PHE 0.024 0.002 PHE B 939 TRP 0.042 0.002 TRP C 633 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (26313) covalent geometry : angle 0.67026 / 0.34 (35812) SS BOND : bond 0.01216 / 0.54 ( 39) SS BOND : angle 1.70682 / 0.94 ( 78) hydrogen bonds : bond 0.04245 / 2.79 ( 932) hydrogen bonds : angle 5.66003 / 3.83 ( 2553) link_NAG-ASN : bond 0.00708 / 0.41 ( 54) link_NAG-ASN : angle 4.28897 / 2.88 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 330 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.7614 (pt) cc_final: 0.7206 (tt) REVERT: C 115 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6251 (mm-40) REVERT: C 298 GLU cc_start: 0.7845 (tt0) cc_final: 0.7427 (tt0) REVERT: C 319 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7126 (ttp-170) REVERT: C 396 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6775 (m-10) REVERT: C 508 TYR cc_start: 0.6558 (m-80) cc_final: 0.6241 (m-10) REVERT: C 751 ASN cc_start: 0.7645 (m-40) cc_final: 0.7392 (m110) REVERT: C 988 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: C 998 THR cc_start: 0.9114 (m) cc_final: 0.8849 (p) REVERT: C 1039 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8069 (mtp180) REVERT: C 1102 TRP cc_start: 0.8237 (m100) cc_final: 0.7174 (m100) REVERT: A 33 THR cc_start: 0.8512 (m) cc_final: 0.8197 (p) REVERT: A 46 SER cc_start: 0.8649 (m) cc_final: 0.8120 (t) REVERT: A 200 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.4939 (t80) REVERT: A 360 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 389 ASP cc_start: 0.7893 (m-30) cc_final: 0.7002 (t0) REVERT: A 558 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8085 (mmtt) REVERT: A 619 GLU cc_start: 0.8366 (tp30) cc_final: 0.8081 (mt-10) REVERT: A 697 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7127 (ttp) REVERT: A 740 MET cc_start: 0.8208 (mmm) cc_final: 0.7973 (tpt) REVERT: A 759 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 779 GLN cc_start: 0.7952 (tp40) cc_final: 0.7513 (tt0) REVERT: A 856 ASN cc_start: 0.7541 (p0) cc_final: 0.7058 (m-40) REVERT: A 1017 GLU cc_start: 0.8418 (tp30) cc_final: 0.8060 (tt0) REVERT: A 1019 ARG cc_start: 0.8568 (tpt170) cc_final: 0.8202 (ttp80) REVERT: B 129 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6282 (mttt) REVERT: B 278 LYS cc_start: 0.8932 (tttt) cc_final: 0.8605 (ttpt) REVERT: B 346 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.6412 (mmm-85) REVERT: B 349 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.6965 (m) REVERT: B 556 ASN cc_start: 0.6355 (m110) cc_final: 0.6016 (t0) REVERT: B 569 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6982 (tp) REVERT: B 636 TYR cc_start: 0.6877 (t80) cc_final: 0.6526 (t80) REVERT: B 754 LEU cc_start: 0.8461 (tt) cc_final: 0.7871 (mt) REVERT: B 1039 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8061 (ptm160) outliers start: 145 outliers final: 97 residues processed: 440 average time/residue: 0.1549 time to fit residues: 111.1167 Evaluate side-chains 405 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 296 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 225 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 625 HIS C1071 GLN A 564 GLN A 784 GLN A1002 GLN B 26 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 853 GLN B 856 ASN B1005 GLN B1058 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.190138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156089 restraints weight = 35786.203| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.18 r_work: 0.3706 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26406 Z= 0.142 Angle : 0.686 16.647 36052 Z= 0.336 Chirality : 0.047 0.654 4194 Planarity : 0.005 0.058 4564 Dihedral : 6.410 107.228 4582 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.31 % Rotamer: Outliers : 4.61 % Allowed : 22.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3159 helix: 1.67 (0.19), residues: 705 sheet: -1.10 (0.19), residues: 714 loop : -1.90 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.022 0.001 TYR A 170 PHE 0.049 0.002 PHE A 127 TRP 0.052 0.002 TRP C 633 HIS 0.010 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (26313) covalent geometry : angle 0.62987 / 0.32 (35812) SS BOND : bond 0.00301 / 0.16 ( 39) SS BOND : angle 1.48428 / 0.79 ( 78) hydrogen bonds : bond 0.04002 / 2.63 ( 932) hydrogen bonds : angle 5.53510 / 3.75 ( 2553) link_NAG-ASN : bond 0.00670 / 0.37 ( 54) link_NAG-ASN : angle 4.00578 / 2.69 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 317 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.7640 (pt) cc_final: 0.7231 (tt) REVERT: C 115 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6823 (mm-40) REVERT: C 508 TYR cc_start: 0.6616 (m-80) cc_final: 0.6317 (m-10) REVERT: C 740 MET cc_start: 0.8578 (tpt) cc_final: 0.8072 (tpt) REVERT: C 936 ASP cc_start: 0.7839 (m-30) cc_final: 0.7639 (m-30) REVERT: C 998 THR cc_start: 0.9121 (m) cc_final: 0.8863 (p) REVERT: C 1039 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8079 (mtp180) REVERT: C 1102 TRP cc_start: 0.8263 (m100) cc_final: 0.7279 (m100) REVERT: A 33 THR cc_start: 0.8486 (m) cc_final: 0.8162 (p) REVERT: A 46 SER cc_start: 0.8688 (m) cc_final: 0.8156 (t) REVERT: A 117 LEU cc_start: 0.8157 (tt) cc_final: 0.7957 (tp) REVERT: A 200 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.4941 (t80) REVERT: A 360 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7488 (t0) REVERT: A 389 ASP cc_start: 0.7897 (m-30) cc_final: 0.6886 (t0) REVERT: A 558 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8111 (mmtt) REVERT: A 619 GLU cc_start: 0.8383 (tp30) cc_final: 0.8068 (mt-10) REVERT: A 759 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7897 (t80) REVERT: A 779 GLN cc_start: 0.7949 (tp40) cc_final: 0.7658 (tt0) REVERT: A 856 ASN cc_start: 0.7451 (p0) cc_final: 0.7051 (m-40) REVERT: A 1017 GLU cc_start: 0.8343 (tp30) cc_final: 0.7975 (tt0) REVERT: A 1019 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8221 (ttp80) REVERT: B 127 PHE cc_start: 0.6446 (t80) cc_final: 0.6026 (t80) REVERT: B 129 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6190 (mtmt) REVERT: B 278 LYS cc_start: 0.9003 (tttt) cc_final: 0.8651 (ttpt) REVERT: B 346 ARG cc_start: 0.7581 (ptp-170) cc_final: 0.6438 (mmm-85) REVERT: B 349 SER cc_start: 0.7312 (m) cc_final: 0.6929 (m) REVERT: B 556 ASN cc_start: 0.6369 (m110) cc_final: 0.6043 (t0) REVERT: B 636 TYR cc_start: 0.6897 (t80) cc_final: 0.6538 (t80) REVERT: B 754 LEU cc_start: 0.8456 (tt) cc_final: 0.7950 (mt) REVERT: B 1039 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8182 (ptm160) outliers start: 128 outliers final: 87 residues processed: 417 average time/residue: 0.1503 time to fit residues: 102.9367 Evaluate side-chains 392 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 298 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 218 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 307 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 856 ASN C1083 HIS A 564 GLN A 784 GLN A1002 GLN B 26 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1005 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154583 restraints weight = 35581.861| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.39 r_work: 0.3695 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26406 Z= 0.127 Angle : 0.669 17.754 36052 Z= 0.328 Chirality : 0.046 0.553 4194 Planarity : 0.005 0.056 4564 Dihedral : 6.279 111.235 4581 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.25 % Favored : 92.56 % Rotamer: Outliers : 4.65 % Allowed : 22.56 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3159 helix: 1.74 (0.19), residues: 711 sheet: -1.11 (0.19), residues: 717 loop : -1.81 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.021 0.001 TYR A 170 PHE 0.036 0.001 PHE C 127 TRP 0.041 0.002 TRP C 633 HIS 0.010 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (26313) covalent geometry : angle 0.61415 / 0.32 (35812) SS BOND : bond 0.00298 / 0.18 ( 39) SS BOND : angle 1.67642 / 1.21 ( 78) hydrogen bonds : bond 0.03833 / 2.51 ( 932) hydrogen bonds : angle 5.43024 / 3.68 ( 2553) link_NAG-ASN : bond 0.00710 / 0.40 ( 54) link_NAG-ASN : angle 3.86618 / 2.59 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 322 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.7594 (pt) cc_final: 0.7198 (tt) REVERT: C 115 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6525 (tp-100) REVERT: C 129 LYS cc_start: 0.8221 (mttt) cc_final: 0.7958 (mmtm) REVERT: C 508 TYR cc_start: 0.6607 (m-80) cc_final: 0.6303 (m-10) REVERT: C 1102 TRP cc_start: 0.8255 (m100) cc_final: 0.7273 (m100) REVERT: A 33 THR cc_start: 0.8524 (m) cc_final: 0.8200 (p) REVERT: A 46 SER cc_start: 0.8692 (m) cc_final: 0.8164 (t) REVERT: A 200 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5069 (t80) REVERT: A 389 ASP cc_start: 0.7953 (m-30) cc_final: 0.6901 (t0) REVERT: A 558 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8148 (mmtt) REVERT: A 619 GLU cc_start: 0.8498 (tp30) cc_final: 0.8070 (mt-10) REVERT: A 697 MET cc_start: 0.7773 (ttp) cc_final: 0.7494 (ptm) REVERT: A 779 GLN cc_start: 0.8016 (tp40) cc_final: 0.7693 (tt0) REVERT: A 856 ASN cc_start: 0.7421 (p0) cc_final: 0.7113 (m-40) REVERT: A 1017 GLU cc_start: 0.8382 (tp30) cc_final: 0.7998 (tt0) REVERT: A 1019 ARG cc_start: 0.8640 (tpt170) cc_final: 0.8231 (ttp80) REVERT: B 127 PHE cc_start: 0.6394 (t80) cc_final: 0.6121 (t80) REVERT: B 278 LYS cc_start: 0.8981 (tttt) cc_final: 0.8638 (ttpt) REVERT: B 349 SER cc_start: 0.7321 (OUTLIER) cc_final: 0.6931 (m) REVERT: B 556 ASN cc_start: 0.6405 (m110) cc_final: 0.6060 (t0) REVERT: B 565 PHE cc_start: 0.7266 (m-80) cc_final: 0.7051 (t80) REVERT: B 636 TYR cc_start: 0.6930 (t80) cc_final: 0.6522 (t80) REVERT: B 754 LEU cc_start: 0.8414 (tt) cc_final: 0.7949 (mt) REVERT: B 900 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7420 (mmt) outliers start: 129 outliers final: 98 residues processed: 415 average time/residue: 0.1584 time to fit residues: 107.5772 Evaluate side-chains 406 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 304 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 86 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 90 optimal weight: 0.0770 chunk 298 optimal weight: 3.9990 chunk 261 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 overall best weight: 1.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 751 ASN C1071 GLN A 564 GLN A 762 GLN A 784 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 955 ASN B1011 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.189270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154783 restraints weight = 35785.011| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.35 r_work: 0.3671 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26406 Z= 0.136 Angle : 0.665 17.334 36052 Z= 0.327 Chirality : 0.046 0.452 4194 Planarity : 0.005 0.058 4564 Dihedral : 6.285 105.852 4581 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.47 % Favored : 92.34 % Rotamer: Outliers : 4.43 % Allowed : 22.74 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 3159 helix: 1.73 (0.19), residues: 711 sheet: -1.06 (0.19), residues: 714 loop : -1.77 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.019 0.001 TYR A 170 PHE 0.029 0.001 PHE C 127 TRP 0.021 0.001 TRP A 353 HIS 0.012 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (26313) covalent geometry : angle 0.61529 / 0.32 (35812) SS BOND : bond 0.00310 / 0.17 ( 39) SS BOND : angle 1.50184 / 0.99 ( 78) hydrogen bonds : bond 0.03866 / 2.53 ( 932) hydrogen bonds : angle 5.39643 / 3.66 ( 2553) link_NAG-ASN : bond 0.00714 / 0.38 ( 54) link_NAG-ASN : angle 3.71008 / 2.51 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 314 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TYR cc_start: 0.7063 (m-80) cc_final: 0.6859 (m-80) REVERT: C 101 ILE cc_start: 0.7576 (pt) cc_final: 0.7180 (tt) REVERT: C 115 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7110 (mm-40) REVERT: C 129 LYS cc_start: 0.8218 (mttt) cc_final: 0.7934 (mmtm) REVERT: C 508 TYR cc_start: 0.6624 (m-80) cc_final: 0.6334 (m-10) REVERT: C 740 MET cc_start: 0.8630 (tpt) cc_final: 0.8258 (tpt) REVERT: C 1039 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8097 (mtp180) REVERT: C 1102 TRP cc_start: 0.8266 (m100) cc_final: 0.7284 (m100) REVERT: A 33 THR cc_start: 0.8552 (m) cc_final: 0.8228 (p) REVERT: A 46 SER cc_start: 0.8727 (m) cc_final: 0.8196 (t) REVERT: A 200 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5026 (t80) REVERT: A 303 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 389 ASP cc_start: 0.7955 (m-30) cc_final: 0.6944 (t0) REVERT: A 558 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8140 (mmtt) REVERT: A 619 GLU cc_start: 0.8526 (tp30) cc_final: 0.8064 (mt-10) REVERT: A 697 MET cc_start: 0.7785 (ttp) cc_final: 0.7533 (ptm) REVERT: A 779 GLN cc_start: 0.8053 (tp40) cc_final: 0.7768 (tt0) REVERT: A 856 ASN cc_start: 0.7402 (p0) cc_final: 0.7119 (m-40) REVERT: A 918 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 1017 GLU cc_start: 0.8384 (tp30) cc_final: 0.8047 (tt0) REVERT: A 1019 ARG cc_start: 0.8662 (tpt170) cc_final: 0.8241 (ttp80) REVERT: A 1129 VAL cc_start: 0.7143 (t) cc_final: 0.6863 (t) REVERT: B 127 PHE cc_start: 0.6614 (t80) cc_final: 0.6375 (t80) REVERT: B 129 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6208 (mttt) REVERT: B 278 LYS cc_start: 0.9021 (tttt) cc_final: 0.8678 (ttpt) REVERT: B 340 GLU cc_start: 0.8052 (mp0) cc_final: 0.7826 (mt-10) REVERT: B 346 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6437 (mmm-85) REVERT: B 349 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7013 (m) REVERT: B 556 ASN cc_start: 0.6425 (m110) cc_final: 0.6106 (t0) REVERT: B 565 PHE cc_start: 0.7427 (m-80) cc_final: 0.7223 (t80) REVERT: B 636 TYR cc_start: 0.7102 (t80) cc_final: 0.6586 (t80) REVERT: B 754 LEU cc_start: 0.8453 (tt) cc_final: 0.7980 (mt) REVERT: B 900 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7436 (mmt) outliers start: 123 outliers final: 97 residues processed: 405 average time/residue: 0.1574 time to fit residues: 104.8625 Evaluate side-chains 409 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 303 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 154 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 856 ASN A 360 ASN A 564 GLN A 762 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 542 ASN B 564 GLN ** B1101 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.190370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156130 restraints weight = 35840.231| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.44 r_work: 0.3687 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26406 Z= 0.124 Angle : 0.679 22.751 36052 Z= 0.327 Chirality : 0.050 1.368 4194 Planarity : 0.005 0.058 4564 Dihedral : 6.079 102.556 4580 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.25 % Favored : 92.56 % Rotamer: Outliers : 3.89 % Allowed : 23.78 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3159 helix: 1.83 (0.20), residues: 711 sheet: -1.04 (0.19), residues: 708 loop : -1.70 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.022 0.001 TYR B 170 PHE 0.029 0.001 PHE B 939 TRP 0.026 0.001 TRP A 353 HIS 0.012 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (26313) covalent geometry : angle 0.61675 / 0.31 (35812) SS BOND : bond 0.00259 / 0.14 ( 39) SS BOND : angle 1.33368 / 0.85 ( 78) hydrogen bonds : bond 0.03698 / 2.43 ( 932) hydrogen bonds : angle 5.31879 / 3.60 ( 2553) link_NAG-ASN : bond 0.00749 / 0.42 ( 54) link_NAG-ASN : angle 4.20151 / 2.96 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 320 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TYR cc_start: 0.7045 (m-80) cc_final: 0.6827 (m-80) REVERT: C 101 ILE cc_start: 0.7603 (pt) cc_final: 0.7211 (tt) REVERT: C 129 LYS cc_start: 0.8173 (mttt) cc_final: 0.7828 (mmtm) REVERT: C 365 TYR cc_start: 0.7916 (m-80) cc_final: 0.7527 (m-80) REVERT: C 508 TYR cc_start: 0.6698 (m-80) cc_final: 0.6404 (m-10) REVERT: C 1102 TRP cc_start: 0.8268 (m100) cc_final: 0.7301 (m100) REVERT: A 33 THR cc_start: 0.8610 (m) cc_final: 0.8309 (p) REVERT: A 46 SER cc_start: 0.8705 (m) cc_final: 0.8154 (t) REVERT: A 117 LEU cc_start: 0.8288 (tt) cc_final: 0.8073 (tp) REVERT: A 127 PHE cc_start: 0.7540 (t80) cc_final: 0.7269 (t80) REVERT: A 200 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5038 (t80) REVERT: A 303 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 389 ASP cc_start: 0.7945 (m-30) cc_final: 0.6891 (t0) REVERT: A 558 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8133 (mmtt) REVERT: A 619 GLU cc_start: 0.8554 (tp30) cc_final: 0.8142 (mt-10) REVERT: A 697 MET cc_start: 0.7892 (ttp) cc_final: 0.7623 (ptm) REVERT: A 779 GLN cc_start: 0.8039 (tp40) cc_final: 0.7797 (tt0) REVERT: A 856 ASN cc_start: 0.7534 (p0) cc_final: 0.7312 (m-40) REVERT: A 1017 GLU cc_start: 0.8369 (tp30) cc_final: 0.7953 (tt0) REVERT: A 1019 ARG cc_start: 0.8661 (tpt170) cc_final: 0.8189 (ttp80) REVERT: A 1129 VAL cc_start: 0.7098 (t) cc_final: 0.6799 (t) REVERT: B 129 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6107 (ttmt) REVERT: B 278 LYS cc_start: 0.8975 (tttt) cc_final: 0.8626 (ttpt) REVERT: B 346 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6378 (mmm-85) REVERT: B 349 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6970 (m) REVERT: B 556 ASN cc_start: 0.6399 (m110) cc_final: 0.6060 (t0) REVERT: B 568 ASP cc_start: 0.5887 (p0) cc_final: 0.5637 (p0) REVERT: B 636 TYR cc_start: 0.7112 (t80) cc_final: 0.6588 (t80) REVERT: B 754 LEU cc_start: 0.8424 (tt) cc_final: 0.7900 (mt) REVERT: B 900 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7540 (mmt) REVERT: B 1136 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7365 (p) outliers start: 108 outliers final: 87 residues processed: 397 average time/residue: 0.1546 time to fit residues: 100.5248 Evaluate side-chains 397 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 303 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 625 HIS C 751 ASN C1071 GLN A 134 GLN A 564 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 564 GLN B 774 GLN B 856 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.190032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155043 restraints weight = 35731.615| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.34 r_work: 0.3683 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26406 Z= 0.125 Angle : 0.665 17.655 36052 Z= 0.326 Chirality : 0.050 1.288 4194 Planarity : 0.005 0.060 4564 Dihedral : 5.938 97.913 4580 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.60 % Favored : 92.24 % Rotamer: Outliers : 3.96 % Allowed : 23.96 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3159 helix: 1.87 (0.20), residues: 711 sheet: -1.01 (0.19), residues: 708 loop : -1.67 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.019 0.001 TYR A 170 PHE 0.030 0.001 PHE B 939 TRP 0.025 0.001 TRP A 353 HIS 0.013 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (26313) covalent geometry : angle 0.61149 / 0.31 (35812) SS BOND : bond 0.00259 / 0.13 ( 39) SS BOND : angle 1.30714 / 0.83 ( 78) hydrogen bonds : bond 0.03684 / 2.41 ( 932) hydrogen bonds : angle 5.29737 / 3.59 ( 2553) link_NAG-ASN : bond 0.00894 / 0.60 ( 54) link_NAG-ASN : angle 3.85196 / 2.67 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 304 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TYR cc_start: 0.7056 (m-80) cc_final: 0.6845 (m-80) REVERT: C 101 ILE cc_start: 0.7592 (pt) cc_final: 0.7188 (tt) REVERT: C 129 LYS cc_start: 0.8120 (mttt) cc_final: 0.7806 (mmtm) REVERT: C 508 TYR cc_start: 0.6672 (m-80) cc_final: 0.6395 (m-10) REVERT: C 1102 TRP cc_start: 0.8255 (m100) cc_final: 0.7248 (m100) REVERT: A 33 THR cc_start: 0.8608 (m) cc_final: 0.8309 (p) REVERT: A 46 SER cc_start: 0.8740 (m) cc_final: 0.8214 (t) REVERT: A 117 LEU cc_start: 0.8323 (tt) cc_final: 0.8086 (tp) REVERT: A 127 PHE cc_start: 0.7645 (t80) cc_final: 0.7389 (t80) REVERT: A 200 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.4878 (t80) REVERT: A 303 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 389 ASP cc_start: 0.7904 (m-30) cc_final: 0.6899 (t0) REVERT: A 558 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8121 (mmtt) REVERT: A 619 GLU cc_start: 0.8498 (tp30) cc_final: 0.8111 (mt-10) REVERT: A 697 MET cc_start: 0.7920 (ttp) cc_final: 0.7679 (ptm) REVERT: A 779 GLN cc_start: 0.8055 (tp40) cc_final: 0.7851 (tt0) REVERT: A 856 ASN cc_start: 0.7512 (p0) cc_final: 0.7298 (m-40) REVERT: A 1017 GLU cc_start: 0.8376 (tp30) cc_final: 0.7979 (tt0) REVERT: A 1019 ARG cc_start: 0.8656 (tpt170) cc_final: 0.8195 (ttp80) REVERT: A 1039 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8450 (ptm160) REVERT: A 1129 VAL cc_start: 0.7108 (t) cc_final: 0.6804 (t) REVERT: B 127 PHE cc_start: 0.6397 (t80) cc_final: 0.5078 (t80) REVERT: B 278 LYS cc_start: 0.8984 (tttt) cc_final: 0.8664 (ttpt) REVERT: B 349 SER cc_start: 0.7426 (m) cc_final: 0.7017 (m) REVERT: B 556 ASN cc_start: 0.6411 (m110) cc_final: 0.6098 (t0) REVERT: B 565 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6847 (t80) REVERT: B 568 ASP cc_start: 0.6039 (p0) cc_final: 0.5807 (p0) REVERT: B 636 TYR cc_start: 0.7190 (t80) cc_final: 0.6635 (t80) REVERT: B 754 LEU cc_start: 0.8376 (tt) cc_final: 0.7892 (mt) REVERT: B 900 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7492 (mmt) REVERT: B 1136 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7342 (p) outliers start: 110 outliers final: 94 residues processed: 384 average time/residue: 0.1477 time to fit residues: 94.6531 Evaluate side-chains 393 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 293 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 101 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 271 optimal weight: 0.0030 chunk 51 optimal weight: 9.9990 chunk 308 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 overall best weight: 0.7512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 625 HIS A 207 HIS A 564 GLN A1002 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 564 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** 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 = 0.4234 r_free = 0.4234 target = 0.190687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155384 restraints weight = 35567.795| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.31 r_work: 0.3692 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26406 Z= 0.120 Angle : 0.658 17.652 36052 Z= 0.323 Chirality : 0.049 1.147 4194 Planarity : 0.005 0.058 4564 Dihedral : 5.822 94.941 4580 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.41 % Favored : 92.43 % Rotamer: Outliers : 3.78 % Allowed : 24.14 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3159 helix: 1.91 (0.20), residues: 711 sheet: -0.99 (0.19), residues: 708 loop : -1.65 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.022 0.001 TYR B 170 PHE 0.030 0.001 PHE B 939 TRP 0.024 0.001 TRP A 353 HIS 0.012 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (26313) covalent geometry : angle 0.60591 / 0.31 (35812) SS BOND : bond 0.00251 / 0.13 ( 39) SS BOND : angle 1.29241 / 0.81 ( 78) hydrogen bonds : bond 0.03615 / 2.37 ( 932) hydrogen bonds : angle 5.27364 / 3.58 ( 2553) link_NAG-ASN : bond 0.00804 / 0.51 ( 54) link_NAG-ASN : angle 3.77515 / 2.61 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7421.33 seconds wall clock time: 127 minutes 49.58 seconds (7669.58 seconds total)