Starting phenix.real_space_refine on Sat Jul 4 22:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwk_23548/07_2026/7lwk_23548.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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 105 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 23847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 23847 At special positions: 0 Unit cell: (133.625, 137.901, 176.385, 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 105 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.94 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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 C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 908.9 milliseconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 49 sheets defined 26.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.710A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.519A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.671A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.544A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.639A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.021A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.772A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.936A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.816A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.725A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.603A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.262A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.784A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.715A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.814A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.010A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.820A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.640A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 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 913 through 919 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.538A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.190A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.505A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.749A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.998A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.771A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.467A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.726A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.801A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.962A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.112A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.720A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.736A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.590A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.269A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.284A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.284A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.874A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.713A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.484A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.636A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.824A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.876A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.716A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.624A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.866A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.964A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.472A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.742A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.026A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.569A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2907 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: 6.41 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6434 1.33 - 1.46: 4509 1.46 - 1.58: 13294 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.60e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.42e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 23994 1.91 - 3.82: 8097 3.82 - 5.72: 983 5.72 - 7.63: 58 7.63 - 9.54: 12 Bond angle restraints: 33144 Sorted by residual: angle pdb=" CA PHE C 133 " pdb=" CB PHE C 133 " pdb=" CG PHE C 133 " ideal model delta sigma weight residual 113.80 119.63 -5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA PHE C 135 " pdb=" CB PHE C 135 " pdb=" CG PHE C 135 " ideal model delta sigma weight residual 113.80 119.47 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" N MET C1050 " pdb=" CA MET C1050 " pdb=" CB MET C1050 " ideal model delta sigma weight residual 111.56 103.09 8.47 1.52e+00 4.33e-01 3.10e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.09e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13330 17.97 - 35.95: 746 35.95 - 53.92: 116 53.92 - 71.89: 57 71.89 - 89.87: 28 Dihedral angle restraints: 14277 sinusoidal: 5550 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.38 85.38 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.90 77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.64 71.64 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 14274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2220 0.078 - 0.157: 1322 0.157 - 0.235: 274 0.235 - 0.314: 51 0.314 - 0.392: 9 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA SER C 112 " pdb=" N SER C 112 " pdb=" C SER C 112 " pdb=" CB SER C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.143 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" CG ASN C 165 " 0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.137 2.00e-02 2.50e+03 1.46e-01 2.68e+02 pdb=" CG ASN C 331 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.102 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" CG ASN A 709 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.129 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11189 2.99 - 3.46: 22366 3.46 - 3.94: 39653 3.94 - 4.42: 44137 4.42 - 4.90: 75147 Nonbonded interactions: 192492 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.519 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.535 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.540 3.040 ... (remaining 192487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.870 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.940 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.013 0.088 24435 Z= 0.768 Angle : 1.789 9.539 33312 Z= 1.198 Chirality : 0.096 0.392 3876 Planarity : 0.013 0.159 4251 Dihedral : 13.021 89.865 8538 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 0.65 % Allowed : 1.98 % Favored : 97.37 % Cbeta Deviations : 0.11 % 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: -0.78 (0.14), residues: 2955 helix: -1.14 (0.16), residues: 693 sheet: 0.68 (0.20), residues: 576 loop : -0.62 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 577 TYR 0.148 0.019 TYR B 396 PHE 0.101 0.012 PHE C 718 TRP 0.074 0.020 TRP A 104 HIS 0.010 0.002 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.01326 / 0.77 (24366) covalent geometry : angle 1.77382 / 1.20 (33144) SS BOND : bond 0.01798 / 0.93 ( 39) SS BOND : angle 2.18845 / 1.47 ( 78) hydrogen bonds : bond 0.16793 / 11.18 ( 1058) hydrogen bonds : angle 8.26162 / 5.74 ( 2907) link_NAG-ASN : bond 0.01194 / 0.75 ( 30) link_NAG-ASN : angle 4.60928 / 3.16 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 389 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6923 (p90) cc_final: 0.6099 (p90) REVERT: A 237 ARG cc_start: 0.7509 (mtt90) cc_final: 0.6955 (ttm-80) REVERT: A 239 GLN cc_start: 0.8417 (tt0) cc_final: 0.7980 (tt0) REVERT: A 529 LYS cc_start: 0.7741 (mttt) cc_final: 0.7477 (tptt) REVERT: A 533 LEU cc_start: 0.8255 (tp) cc_final: 0.7651 (mt) REVERT: A 933 LYS cc_start: 0.8313 (mttt) cc_final: 0.7994 (mtpm) REVERT: A 954 GLN cc_start: 0.7921 (mt0) cc_final: 0.7718 (mt0) REVERT: A 1029 MET cc_start: 0.9104 (tpp) cc_final: 0.8764 (tpp) REVERT: B 202 LYS cc_start: 0.7619 (mttm) cc_final: 0.7088 (mttp) REVERT: B 230 PRO cc_start: 0.7918 (Cg_endo) cc_final: 0.7660 (Cg_exo) REVERT: B 239 GLN cc_start: 0.7312 (tt0) cc_final: 0.7025 (tp40) REVERT: B 362 VAL cc_start: 0.7729 (t) cc_final: 0.7483 (m) REVERT: B 436 TRP cc_start: 0.7545 (p90) cc_final: 0.6663 (p90) REVERT: B 462 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7117 (pptt) REVERT: B 511 VAL cc_start: 0.7580 (t) cc_final: 0.7330 (m) REVERT: B 529 LYS cc_start: 0.8125 (mttt) cc_final: 0.7683 (ttpp) REVERT: B 532 ASN cc_start: 0.8057 (t0) cc_final: 0.7647 (p0) REVERT: B 540 ASN cc_start: 0.7980 (t0) cc_final: 0.7764 (t0) REVERT: B 823 PHE cc_start: 0.7901 (m-80) cc_final: 0.7697 (m-80) REVERT: C 41 LYS cc_start: 0.7989 (mttt) cc_final: 0.7600 (mttp) REVERT: C 129 LYS cc_start: 0.6816 (mttm) cc_final: 0.6455 (mmtp) REVERT: C 205 SER cc_start: 0.9245 (p) cc_final: 0.8806 (t) REVERT: C 383 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.6903 (p) REVERT: C 394 ASN cc_start: 0.5500 (m-40) cc_final: 0.5256 (m-40) REVERT: C 425 LEU cc_start: 0.7774 (mt) cc_final: 0.7354 (mt) REVERT: C 434 ILE cc_start: 0.8810 (mt) cc_final: 0.8138 (tp) REVERT: C 529 LYS cc_start: 0.7554 (mttt) cc_final: 0.7213 (mmmm) REVERT: C 586 ASP cc_start: 0.7747 (m-30) cc_final: 0.7378 (m-30) REVERT: C 747 THR cc_start: 0.8584 (m) cc_final: 0.8376 (p) REVERT: C 1029 MET cc_start: 0.9082 (tpp) cc_final: 0.8788 (tpp) outliers start: 17 outliers final: 4 residues processed: 404 average time/residue: 0.5666 time to fit residues: 267.8826 Evaluate side-chains 216 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 121 ASN A 188 ASN A 519 HIS A 580 GLN A 641 ASN A 675 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 188 ASN B 207 HIS B 394 ASN B 501 ASN B 755 GLN B 965 GLN C 121 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.186198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118841 restraints weight = 29074.402| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.54 r_work: 0.3126 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24435 Z= 0.174 Angle : 0.696 11.631 33312 Z= 0.362 Chirality : 0.048 0.207 3876 Planarity : 0.004 0.034 4251 Dihedral : 5.916 50.127 3206 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.75 % Allowed : 7.36 % Favored : 89.89 % 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: 0.27 (0.15), residues: 2955 helix: 0.94 (0.20), residues: 687 sheet: 0.75 (0.19), residues: 657 loop : -0.36 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 357 TYR 0.023 0.002 TYR B 380 PHE 0.016 0.002 PHE B 201 TRP 0.016 0.002 TRP A 64 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (24366) covalent geometry : angle 0.66252 / 0.35 (33144) SS BOND : bond 0.00516 / 0.33 ( 39) SS BOND : angle 2.16626 / 1.52 ( 78) hydrogen bonds : bond 0.05273 / 3.44 ( 1058) hydrogen bonds : angle 6.34347 / 4.36 ( 2907) link_NAG-ASN : bond 0.00299 / 0.17 ( 30) link_NAG-ASN : angle 3.65665 / 2.39 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7274 (p0) cc_final: 0.6908 (p0) REVERT: A 190 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7340 (mmt-90) REVERT: A 207 HIS cc_start: 0.7542 (p90) cc_final: 0.7147 (p90) REVERT: A 237 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7316 (ttm-80) REVERT: A 239 GLN cc_start: 0.8665 (tt0) cc_final: 0.8323 (tt0) REVERT: A 359 SER cc_start: 0.7954 (p) cc_final: 0.7701 (t) REVERT: A 529 LYS cc_start: 0.7938 (mttt) cc_final: 0.7587 (tptt) REVERT: A 533 LEU cc_start: 0.8136 (tp) cc_final: 0.7773 (mt) REVERT: A 651 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9052 (mt) REVERT: A 796 ASP cc_start: 0.7757 (t0) cc_final: 0.7551 (t0) REVERT: A 954 GLN cc_start: 0.8453 (mt0) cc_final: 0.8248 (mt0) REVERT: A 1029 MET cc_start: 0.9208 (tpp) cc_final: 0.8945 (tpp) REVERT: B 33 THR cc_start: 0.8193 (p) cc_final: 0.7805 (p) REVERT: B 54 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 202 LYS cc_start: 0.7692 (mttm) cc_final: 0.7221 (mttp) REVERT: B 230 PRO cc_start: 0.7602 (Cg_endo) cc_final: 0.7235 (Cg_exo) REVERT: B 239 GLN cc_start: 0.7652 (tt0) cc_final: 0.7325 (tp40) REVERT: B 436 TRP cc_start: 0.7266 (p90) cc_final: 0.6809 (p-90) REVERT: B 529 LYS cc_start: 0.8235 (mttt) cc_final: 0.7824 (ttpp) REVERT: B 995 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8099 (mtp85) REVERT: C 41 LYS cc_start: 0.8325 (mttt) cc_final: 0.7988 (mttp) REVERT: C 129 LYS cc_start: 0.6885 (mttm) cc_final: 0.6622 (mttp) REVERT: C 205 SER cc_start: 0.9456 (p) cc_final: 0.9219 (t) REVERT: C 278 LYS cc_start: 0.8647 (tttt) cc_final: 0.8390 (tttp) REVERT: C 383 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7287 (p) REVERT: C 396 TYR cc_start: 0.7573 (m-80) cc_final: 0.6781 (m-80) REVERT: C 529 LYS cc_start: 0.7650 (mttt) cc_final: 0.7339 (mmmm) REVERT: C 577 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8326 (ttm-80) REVERT: C 586 ASP cc_start: 0.7983 (m-30) cc_final: 0.7612 (m-30) REVERT: C 675 GLN cc_start: 0.7123 (mt0) cc_final: 0.6708 (pt0) REVERT: C 988 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: C 1010 GLN cc_start: 0.8456 (mt0) cc_final: 0.7810 (pt0) outliers start: 72 outliers final: 22 residues processed: 296 average time/residue: 0.5324 time to fit residues: 186.4342 Evaluate side-chains 225 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 214 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 229 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 314 GLN B 564 GLN B 901 GLN C 66 HIS C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119387 restraints weight = 29104.111| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.57 r_work: 0.3142 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24435 Z= 0.124 Angle : 0.601 11.966 33312 Z= 0.309 Chirality : 0.045 0.241 3876 Planarity : 0.003 0.036 4251 Dihedral : 5.162 29.460 3203 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 9.31 % Favored : 88.25 % 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: 0.55 (0.15), residues: 2955 helix: 1.42 (0.21), residues: 687 sheet: 0.82 (0.19), residues: 618 loop : -0.22 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.021 0.001 TYR B 170 PHE 0.012 0.001 PHE C 643 TRP 0.014 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24366) covalent geometry : angle 0.57092 / 0.30 (33144) SS BOND : bond 0.00419 / 0.27 ( 39) SS BOND : angle 1.73883 / 1.14 ( 78) hydrogen bonds : bond 0.04426 / 2.88 ( 1058) hydrogen bonds : angle 5.97335 / 4.11 ( 2907) link_NAG-ASN : bond 0.01197 / 0.98 ( 30) link_NAG-ASN : angle 3.34075 / 2.43 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7852 (t0) cc_final: 0.7386 (t0) REVERT: A 81 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.6956 (p0) REVERT: A 190 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7294 (mmt-90) REVERT: A 207 HIS cc_start: 0.7431 (p90) cc_final: 0.7082 (p90) REVERT: A 237 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7353 (ttm-80) REVERT: A 239 GLN cc_start: 0.8666 (tt0) cc_final: 0.8273 (tt0) REVERT: A 284 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 347 PHE cc_start: 0.3832 (OUTLIER) cc_final: 0.3492 (t80) REVERT: A 529 LYS cc_start: 0.7956 (mttt) cc_final: 0.7614 (tptt) REVERT: A 531 THR cc_start: 0.8192 (t) cc_final: 0.7859 (p) REVERT: A 533 LEU cc_start: 0.8084 (tp) cc_final: 0.7769 (mt) REVERT: A 796 ASP cc_start: 0.7725 (t0) cc_final: 0.7493 (t0) REVERT: A 954 GLN cc_start: 0.8465 (mt0) cc_final: 0.8256 (mt0) REVERT: A 994 ASP cc_start: 0.8605 (t70) cc_final: 0.8294 (m-30) REVERT: A 1029 MET cc_start: 0.9144 (tpp) cc_final: 0.8914 (tpp) REVERT: B 33 THR cc_start: 0.8217 (p) cc_final: 0.8003 (p) REVERT: B 52 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: B 54 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 202 LYS cc_start: 0.7649 (mttm) cc_final: 0.7134 (mttp) REVERT: B 239 GLN cc_start: 0.7739 (tt0) cc_final: 0.7373 (tp40) REVERT: B 436 TRP cc_start: 0.7310 (p90) cc_final: 0.6924 (p-90) REVERT: B 462 LYS cc_start: 0.7472 (mptp) cc_final: 0.6780 (pptt) REVERT: B 529 LYS cc_start: 0.8276 (mttt) cc_final: 0.7839 (ttpp) REVERT: B 740 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8862 (ttt) REVERT: C 41 LYS cc_start: 0.8278 (mttt) cc_final: 0.7956 (mttp) REVERT: C 102 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5643 (ttm170) REVERT: C 129 LYS cc_start: 0.6855 (mttm) cc_final: 0.6535 (mttp) REVERT: C 278 LYS cc_start: 0.8713 (tttt) cc_final: 0.8419 (tttp) REVERT: C 394 ASN cc_start: 0.6762 (t0) cc_final: 0.6346 (t160) REVERT: C 529 LYS cc_start: 0.7718 (mttt) cc_final: 0.7316 (mmmm) REVERT: C 577 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8231 (ttm-80) REVERT: C 586 ASP cc_start: 0.7820 (m-30) cc_final: 0.7569 (m-30) REVERT: C 675 GLN cc_start: 0.7164 (mt0) cc_final: 0.6748 (tm-30) REVERT: C 825 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8199 (tptp) REVERT: C 988 GLU cc_start: 0.7974 (tp30) cc_final: 0.7709 (tm-30) REVERT: C 1010 GLN cc_start: 0.8452 (mt0) cc_final: 0.7795 (pt0) outliers start: 64 outliers final: 22 residues processed: 258 average time/residue: 0.4884 time to fit residues: 150.0153 Evaluate side-chains 220 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 825 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 35 optimal weight: 40.0000 chunk 204 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS C 901 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.184103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115602 restraints weight = 28948.535| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.45 r_work: 0.3097 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24435 Z= 0.208 Angle : 0.645 13.779 33312 Z= 0.330 Chirality : 0.048 0.324 3876 Planarity : 0.004 0.063 4251 Dihedral : 5.136 31.619 3202 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.43 % Allowed : 9.31 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.36 (0.15), residues: 2955 helix: 1.13 (0.20), residues: 699 sheet: 0.86 (0.20), residues: 582 loop : -0.33 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.021 0.002 TYR B 380 PHE 0.023 0.002 PHE C 855 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (24366) covalent geometry : angle 0.61763 / 0.32 (33144) SS BOND : bond 0.00770 / 0.46 ( 39) SS BOND : angle 1.90635 / 1.29 ( 78) hydrogen bonds : bond 0.05065 / 3.32 ( 1058) hydrogen bonds : angle 6.00348 / 4.13 ( 2907) link_NAG-ASN : bond 0.00613 / 0.48 ( 30) link_NAG-ASN : angle 3.21465 / 2.27 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 203 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7845 (t0) cc_final: 0.7374 (t0) REVERT: A 207 HIS cc_start: 0.7452 (p90) cc_final: 0.7135 (p90) REVERT: A 237 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7428 (ttm-80) REVERT: A 239 GLN cc_start: 0.8780 (tt0) cc_final: 0.8320 (tt0) REVERT: A 284 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 529 LYS cc_start: 0.7907 (mttt) cc_final: 0.7643 (tptt) REVERT: A 533 LEU cc_start: 0.8086 (tp) cc_final: 0.7708 (mt) REVERT: A 651 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9123 (mm) REVERT: A 740 MET cc_start: 0.9036 (ttp) cc_final: 0.8831 (ttt) REVERT: A 796 ASP cc_start: 0.7966 (t0) cc_final: 0.7740 (t0) REVERT: A 1029 MET cc_start: 0.9243 (tpp) cc_final: 0.9042 (tpp) REVERT: B 33 THR cc_start: 0.8233 (p) cc_final: 0.7962 (p) REVERT: B 52 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 54 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 239 GLN cc_start: 0.7836 (tt0) cc_final: 0.7527 (tt0) REVERT: B 436 TRP cc_start: 0.7315 (p90) cc_final: 0.7036 (p-90) REVERT: B 462 LYS cc_start: 0.7416 (mptp) cc_final: 0.6740 (pptt) REVERT: B 529 LYS cc_start: 0.8217 (mttt) cc_final: 0.7825 (ttpp) REVERT: B 560 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 740 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8843 (ttt) REVERT: C 41 LYS cc_start: 0.8388 (mttt) cc_final: 0.8066 (mttp) REVERT: C 102 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.5707 (ttm170) REVERT: C 129 LYS cc_start: 0.6897 (mttm) cc_final: 0.6527 (mttp) REVERT: C 165 ASN cc_start: 0.5350 (OUTLIER) cc_final: 0.5138 (t0) REVERT: C 231 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (pt) REVERT: C 278 LYS cc_start: 0.8732 (tttt) cc_final: 0.8405 (tttp) REVERT: C 357 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7906 (tpp80) REVERT: C 394 ASN cc_start: 0.6930 (t0) cc_final: 0.6391 (t160) REVERT: C 396 TYR cc_start: 0.8057 (m-80) cc_final: 0.7553 (m-80) REVERT: C 586 ASP cc_start: 0.7930 (m-30) cc_final: 0.7661 (m-30) REVERT: C 988 GLU cc_start: 0.7868 (tp30) cc_final: 0.7616 (tm-30) REVERT: C 1010 GLN cc_start: 0.8459 (mt0) cc_final: 0.7786 (pt0) outliers start: 90 outliers final: 41 residues processed: 259 average time/residue: 0.4706 time to fit residues: 145.8022 Evaluate side-chains 231 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 157 optimal weight: 0.4980 chunk 194 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 334 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.185849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118390 restraints weight = 28815.802| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.42 r_work: 0.3140 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24435 Z= 0.131 Angle : 0.569 13.768 33312 Z= 0.292 Chirality : 0.046 0.334 3876 Planarity : 0.004 0.052 4251 Dihedral : 4.738 20.826 3201 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 10.95 % Favored : 86.50 % 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: 0.49 (0.15), residues: 2955 helix: 1.39 (0.21), residues: 702 sheet: 0.80 (0.20), residues: 582 loop : -0.27 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.023 0.001 TYR B 170 PHE 0.014 0.001 PHE C 643 TRP 0.013 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24366) covalent geometry : angle 0.54743 / 0.29 (33144) SS BOND : bond 0.00505 / 0.34 ( 39) SS BOND : angle 1.92952 / 1.25 ( 78) hydrogen bonds : bond 0.04213 / 2.74 ( 1058) hydrogen bonds : angle 5.76486 / 3.96 ( 2907) link_NAG-ASN : bond 0.00496 / 0.39 ( 30) link_NAG-ASN : angle 2.53238 / 1.84 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7900 (t0) cc_final: 0.7430 (t0) REVERT: A 237 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7351 (ttm-80) REVERT: A 239 GLN cc_start: 0.8700 (tt0) cc_final: 0.8270 (tt0) REVERT: A 284 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 529 LYS cc_start: 0.7901 (mttt) cc_final: 0.7634 (tptt) REVERT: A 533 LEU cc_start: 0.7966 (tp) cc_final: 0.7678 (mt) REVERT: A 796 ASP cc_start: 0.7817 (t0) cc_final: 0.7602 (t0) REVERT: A 994 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: A 1029 MET cc_start: 0.9173 (tpp) cc_final: 0.8948 (tpp) REVERT: B 239 GLN cc_start: 0.7848 (tt0) cc_final: 0.7554 (tt0) REVERT: B 436 TRP cc_start: 0.7396 (p90) cc_final: 0.7009 (p-90) REVERT: B 462 LYS cc_start: 0.7413 (mptp) cc_final: 0.6717 (pptt) REVERT: B 529 LYS cc_start: 0.8244 (mttt) cc_final: 0.7828 (ttpp) REVERT: B 740 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8856 (ttp) REVERT: C 41 LYS cc_start: 0.8295 (mttt) cc_final: 0.7927 (mttp) REVERT: C 102 ARG cc_start: 0.5785 (OUTLIER) cc_final: 0.5551 (ttm170) REVERT: C 121 ASN cc_start: 0.6616 (m-40) cc_final: 0.6265 (m110) REVERT: C 129 LYS cc_start: 0.6970 (mttm) cc_final: 0.6605 (mmtp) REVERT: C 231 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8146 (pt) REVERT: C 278 LYS cc_start: 0.8706 (tttt) cc_final: 0.8386 (tttp) REVERT: C 394 ASN cc_start: 0.6880 (t0) cc_final: 0.6509 (t160) REVERT: C 396 TYR cc_start: 0.7958 (m-80) cc_final: 0.7583 (m-10) REVERT: C 675 GLN cc_start: 0.7261 (mt0) cc_final: 0.6783 (pt0) REVERT: C 988 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: C 1010 GLN cc_start: 0.8284 (mt0) cc_final: 0.7749 (pt0) outliers start: 67 outliers final: 29 residues processed: 236 average time/residue: 0.4362 time to fit residues: 123.6962 Evaluate side-chains 220 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 104 optimal weight: 0.1980 chunk 213 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113567 restraints weight = 29015.702| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.17 r_work: 0.3099 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 24435 Z= 0.256 Angle : 0.672 14.266 33312 Z= 0.343 Chirality : 0.049 0.327 3876 Planarity : 0.004 0.047 4251 Dihedral : 5.027 24.222 3201 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 10.56 % Favored : 86.00 % 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: 0.15 (0.15), residues: 2955 helix: 1.03 (0.20), residues: 705 sheet: 0.57 (0.19), residues: 618 loop : -0.47 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.023 0.002 TYR B 265 PHE 0.021 0.002 PHE C 855 TRP 0.010 0.002 TRP B 886 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (24366) covalent geometry : angle 0.64480 / 0.34 (33144) SS BOND : bond 0.00652 / 0.39 ( 39) SS BOND : angle 2.52204 / 1.57 ( 78) hydrogen bonds : bond 0.05318 / 3.48 ( 1058) hydrogen bonds : angle 6.00122 / 4.13 ( 2907) link_NAG-ASN : bond 0.00500 / 0.38 ( 30) link_NAG-ASN : angle 2.87807 / 2.05 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 188 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7778 (t0) cc_final: 0.7316 (t0) REVERT: A 237 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7400 (ttm-80) REVERT: A 239 GLN cc_start: 0.8732 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 529 LYS cc_start: 0.7907 (mttt) cc_final: 0.7620 (tptt) REVERT: A 533 LEU cc_start: 0.8087 (tp) cc_final: 0.7775 (mt) REVERT: A 651 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9154 (mm) REVERT: A 675 GLN cc_start: 0.7142 (pp30) cc_final: 0.6784 (pp30) REVERT: A 1029 MET cc_start: 0.9251 (tpp) cc_final: 0.9017 (tpp) REVERT: B 52 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: B 54 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 239 GLN cc_start: 0.7845 (tt0) cc_final: 0.7568 (tt0) REVERT: B 324 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: B 436 TRP cc_start: 0.7379 (p90) cc_final: 0.6972 (p-90) REVERT: B 529 LYS cc_start: 0.8315 (mttt) cc_final: 0.7909 (ttpp) REVERT: B 740 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8779 (ttp) REVERT: C 41 LYS cc_start: 0.8434 (mttt) cc_final: 0.7984 (mttp) REVERT: C 121 ASN cc_start: 0.6861 (m-40) cc_final: 0.6443 (m-40) REVERT: C 129 LYS cc_start: 0.7034 (mttm) cc_final: 0.6630 (mmtp) REVERT: C 231 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8192 (pt) REVERT: C 278 LYS cc_start: 0.8781 (tttt) cc_final: 0.8470 (tttp) REVERT: C 357 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7626 (tpp-160) REVERT: C 394 ASN cc_start: 0.7096 (t0) cc_final: 0.6667 (t160) REVERT: C 396 TYR cc_start: 0.7989 (m-80) cc_final: 0.7672 (m-80) REVERT: C 988 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (tm-30) outliers start: 90 outliers final: 46 residues processed: 240 average time/residue: 0.4964 time to fit residues: 142.2798 Evaluate side-chains 223 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115631 restraints weight = 28887.883| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.53 r_work: 0.3051 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 24435 Z= 0.222 Angle : 0.635 13.166 33312 Z= 0.327 Chirality : 0.048 0.322 3876 Planarity : 0.004 0.049 4251 Dihedral : 4.940 23.017 3201 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.94 % Allowed : 11.52 % Favored : 85.55 % 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: 0.19 (0.15), residues: 2955 helix: 1.22 (0.20), residues: 681 sheet: 0.47 (0.19), residues: 648 loop : -0.45 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.025 0.002 TYR B 170 PHE 0.015 0.002 PHE A 643 TRP 0.012 0.002 TRP A 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (24366) covalent geometry : angle 0.61095 / 0.32 (33144) SS BOND : bond 0.00590 / 0.37 ( 39) SS BOND : angle 2.26983 / 1.42 ( 78) hydrogen bonds : bond 0.04963 / 3.25 ( 1058) hydrogen bonds : angle 5.91769 / 4.07 ( 2907) link_NAG-ASN : bond 0.00401 / 0.31 ( 30) link_NAG-ASN : angle 2.72586 / 1.93 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 183 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7923 (t0) cc_final: 0.7476 (t0) REVERT: A 61 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 237 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7448 (ttm-80) REVERT: A 239 GLN cc_start: 0.8730 (tt0) cc_final: 0.8445 (tt0) REVERT: A 529 LYS cc_start: 0.7920 (mttt) cc_final: 0.7594 (tptt) REVERT: A 533 LEU cc_start: 0.8152 (tp) cc_final: 0.7735 (mt) REVERT: A 651 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 675 GLN cc_start: 0.7189 (pp30) cc_final: 0.6840 (pp30) REVERT: A 1029 MET cc_start: 0.9269 (tpp) cc_final: 0.9069 (tpp) REVERT: B 54 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 207 HIS cc_start: 0.7742 (m90) cc_final: 0.7322 (m-70) REVERT: B 239 GLN cc_start: 0.7862 (tt0) cc_final: 0.7585 (tt0) REVERT: B 324 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: B 436 TRP cc_start: 0.7370 (p90) cc_final: 0.6994 (p-90) REVERT: B 462 LYS cc_start: 0.7513 (mptp) cc_final: 0.6787 (pptt) REVERT: B 529 LYS cc_start: 0.8314 (mttt) cc_final: 0.7905 (ttpp) REVERT: B 740 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8895 (ttt) REVERT: B 786 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (pttt) REVERT: C 41 LYS cc_start: 0.8457 (mttt) cc_final: 0.8059 (mttp) REVERT: C 121 ASN cc_start: 0.6997 (m-40) cc_final: 0.6651 (m-40) REVERT: C 129 LYS cc_start: 0.7034 (mttm) cc_final: 0.6692 (mmtp) REVERT: C 130 VAL cc_start: 0.6817 (t) cc_final: 0.6432 (m) REVERT: C 231 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8210 (pt) REVERT: C 278 LYS cc_start: 0.8767 (tttt) cc_final: 0.8440 (tttp) REVERT: C 394 ASN cc_start: 0.7109 (t0) cc_final: 0.6693 (t160) REVERT: C 396 TYR cc_start: 0.8040 (m-80) cc_final: 0.7708 (m-80) REVERT: C 453 PHE cc_start: 0.6234 (p90) cc_final: 0.5978 (p90) REVERT: C 505 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6476 (t80) REVERT: C 988 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7619 (tm-30) outliers start: 77 outliers final: 40 residues processed: 231 average time/residue: 0.4881 time to fit residues: 135.6667 Evaluate side-chains 219 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 276 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 564 GLN B 762 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124471 restraints weight = 28757.744| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.49 r_work: 0.3170 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24435 Z= 0.111 Angle : 0.542 10.311 33312 Z= 0.280 Chirality : 0.045 0.301 3876 Planarity : 0.004 0.067 4251 Dihedral : 4.502 19.496 3201 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.02 % Allowed : 12.36 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2955 helix: 1.98 (0.21), residues: 645 sheet: 0.39 (0.18), residues: 699 loop : -0.30 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.023 0.001 TYR B 170 PHE 0.016 0.001 PHE C 643 TRP 0.015 0.001 TRP A 436 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24366) covalent geometry : angle 0.52127 / 0.27 (33144) SS BOND : bond 0.00439 / 0.31 ( 39) SS BOND : angle 2.03538 / 1.27 ( 78) hydrogen bonds : bond 0.03797 / 2.46 ( 1058) hydrogen bonds : angle 5.57584 / 3.83 ( 2907) link_NAG-ASN : bond 0.00332 / 0.25 ( 30) link_NAG-ASN : angle 2.26598 / 1.63 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8876 (p) cc_final: 0.8628 (t) REVERT: A 53 ASP cc_start: 0.7861 (t0) cc_final: 0.7405 (t0) REVERT: A 61 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7022 (t0) REVERT: A 237 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7474 (ttm-80) REVERT: A 239 GLN cc_start: 0.8724 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 529 LYS cc_start: 0.7844 (mttt) cc_final: 0.7585 (tptt) REVERT: A 790 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (ptmm) REVERT: A 994 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: B 239 GLN cc_start: 0.7825 (tt0) cc_final: 0.7555 (tt0) REVERT: B 436 TRP cc_start: 0.7357 (p90) cc_final: 0.7051 (p-90) REVERT: B 462 LYS cc_start: 0.7533 (mptp) cc_final: 0.6831 (pptt) REVERT: B 529 LYS cc_start: 0.8242 (mttt) cc_final: 0.7883 (ttpp) REVERT: B 540 ASN cc_start: 0.7775 (t0) cc_final: 0.7540 (p0) REVERT: B 583 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: B 740 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8895 (ttp) REVERT: C 41 LYS cc_start: 0.8426 (mttt) cc_final: 0.8018 (mttp) REVERT: C 121 ASN cc_start: 0.6866 (m-40) cc_final: 0.6502 (m-40) REVERT: C 231 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (pt) REVERT: C 278 LYS cc_start: 0.8749 (tttt) cc_final: 0.8422 (tttp) REVERT: C 453 PHE cc_start: 0.6284 (p90) cc_final: 0.5986 (p90) REVERT: C 505 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6548 (t80) REVERT: C 988 GLU cc_start: 0.7742 (tp30) cc_final: 0.7501 (tm-30) REVERT: C 1010 GLN cc_start: 0.8254 (mt0) cc_final: 0.8043 (mm-40) outliers start: 53 outliers final: 33 residues processed: 231 average time/residue: 0.4795 time to fit residues: 133.8034 Evaluate side-chains 221 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 23 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 0.0020 chunk 2 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.186742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124904 restraints weight = 28775.702| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.52 r_work: 0.3152 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24435 Z= 0.118 Angle : 0.551 10.180 33312 Z= 0.283 Chirality : 0.045 0.301 3876 Planarity : 0.004 0.062 4251 Dihedral : 4.427 20.538 3201 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.79 % Allowed : 13.08 % Favored : 85.13 % 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: 0.58 (0.15), residues: 2955 helix: 2.05 (0.21), residues: 645 sheet: 0.43 (0.18), residues: 699 loop : -0.28 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.022 0.001 TYR B 380 PHE 0.024 0.001 PHE A 855 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (24366) covalent geometry : angle 0.53206 / 0.28 (33144) SS BOND : bond 0.00420 / 0.30 ( 39) SS BOND : angle 1.95995 / 1.22 ( 78) hydrogen bonds : bond 0.03871 / 2.51 ( 1058) hydrogen bonds : angle 5.54023 / 3.81 ( 2907) link_NAG-ASN : bond 0.00336 / 0.26 ( 30) link_NAG-ASN : angle 2.21768 / 1.61 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8862 (p) cc_final: 0.8629 (t) REVERT: A 53 ASP cc_start: 0.7851 (t0) cc_final: 0.7368 (t70) REVERT: A 237 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7424 (ttm-80) REVERT: A 239 GLN cc_start: 0.8724 (tt0) cc_final: 0.8354 (tm-30) REVERT: A 310 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8623 (ptmt) REVERT: A 529 LYS cc_start: 0.7909 (mttt) cc_final: 0.7676 (tptt) REVERT: A 531 THR cc_start: 0.8169 (t) cc_final: 0.7878 (p) REVERT: A 950 ASP cc_start: 0.8500 (m-30) cc_final: 0.8221 (m-30) REVERT: A 994 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: B 207 HIS cc_start: 0.7872 (m-70) cc_final: 0.7518 (m-70) REVERT: B 239 GLN cc_start: 0.7811 (tt0) cc_final: 0.7535 (tt0) REVERT: B 436 TRP cc_start: 0.7323 (p90) cc_final: 0.7011 (p-90) REVERT: B 462 LYS cc_start: 0.7466 (mptp) cc_final: 0.6750 (pptt) REVERT: B 529 LYS cc_start: 0.8194 (mttt) cc_final: 0.7839 (ttpp) REVERT: B 540 ASN cc_start: 0.7772 (t0) cc_final: 0.7504 (p0) REVERT: B 583 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: B 740 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8816 (ttp) REVERT: C 41 LYS cc_start: 0.8397 (mttt) cc_final: 0.7983 (mttp) REVERT: C 121 ASN cc_start: 0.6868 (m-40) cc_final: 0.6481 (m-40) REVERT: C 231 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8004 (pt) REVERT: C 278 LYS cc_start: 0.8705 (tttt) cc_final: 0.8359 (tttp) REVERT: C 453 PHE cc_start: 0.6272 (p90) cc_final: 0.5975 (p90) REVERT: C 505 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6549 (t80) REVERT: C 511 VAL cc_start: 0.8324 (t) cc_final: 0.8076 (m) REVERT: C 988 GLU cc_start: 0.7749 (tp30) cc_final: 0.7501 (tm-30) REVERT: C 1010 GLN cc_start: 0.8272 (mt0) cc_final: 0.8037 (mm-40) REVERT: C 1050 MET cc_start: 0.8852 (mtp) cc_final: 0.8623 (mtp) outliers start: 47 outliers final: 34 residues processed: 214 average time/residue: 0.4617 time to fit residues: 120.2867 Evaluate side-chains 219 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 132 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 183 optimal weight: 0.8980 chunk 136 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118706 restraints weight = 28855.607| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.55 r_work: 0.3090 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24435 Z= 0.147 Angle : 0.567 9.832 33312 Z= 0.292 Chirality : 0.046 0.311 3876 Planarity : 0.004 0.061 4251 Dihedral : 4.492 23.667 3201 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.72 % Allowed : 13.46 % Favored : 84.82 % 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: 0.53 (0.15), residues: 2955 helix: 1.92 (0.21), residues: 648 sheet: 0.42 (0.18), residues: 702 loop : -0.30 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.024 0.001 TYR B 170 PHE 0.020 0.001 PHE C 643 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24366) covalent geometry : angle 0.54721 / 0.29 (33144) SS BOND : bond 0.00523 / 0.35 ( 39) SS BOND : angle 2.09815 / 1.32 ( 78) hydrogen bonds : bond 0.04241 / 2.77 ( 1058) hydrogen bonds : angle 5.61300 / 3.86 ( 2907) link_NAG-ASN : bond 0.00342 / 0.27 ( 30) link_NAG-ASN : angle 2.22575 / 1.61 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7924 (t0) cc_final: 0.7472 (t0) REVERT: A 237 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7527 (ttm-80) REVERT: A 239 GLN cc_start: 0.8765 (tt0) cc_final: 0.8418 (tm-30) REVERT: A 310 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8625 (ptmt) REVERT: A 356 LYS cc_start: 0.7041 (tptt) cc_final: 0.6687 (tptm) REVERT: A 529 LYS cc_start: 0.7916 (mttt) cc_final: 0.7668 (tptt) REVERT: A 531 THR cc_start: 0.8163 (t) cc_final: 0.7887 (p) REVERT: A 950 ASP cc_start: 0.8613 (m-30) cc_final: 0.8344 (m-30) REVERT: A 994 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: B 207 HIS cc_start: 0.7813 (m90) cc_final: 0.7544 (m-70) REVERT: B 239 GLN cc_start: 0.7873 (tt0) cc_final: 0.7646 (tt0) REVERT: B 436 TRP cc_start: 0.7313 (p90) cc_final: 0.7026 (p-90) REVERT: B 529 LYS cc_start: 0.8221 (mttt) cc_final: 0.7787 (ttpp) REVERT: B 583 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: B 740 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8841 (ttp) REVERT: C 41 LYS cc_start: 0.8451 (mttt) cc_final: 0.7985 (mttp) REVERT: C 121 ASN cc_start: 0.6863 (m-40) cc_final: 0.6505 (m-40) REVERT: C 128 ILE cc_start: 0.8144 (mt) cc_final: 0.7911 (mp) REVERT: C 129 LYS cc_start: 0.7071 (mttm) cc_final: 0.6729 (mttp) REVERT: C 131 CYS cc_start: 0.4307 (m) cc_final: 0.3269 (m) REVERT: C 231 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8009 (pt) REVERT: C 278 LYS cc_start: 0.8759 (tttt) cc_final: 0.8425 (tttp) REVERT: C 453 PHE cc_start: 0.6257 (p90) cc_final: 0.5921 (p90) REVERT: C 505 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6501 (t80) REVERT: C 511 VAL cc_start: 0.8271 (t) cc_final: 0.8028 (m) REVERT: C 988 GLU cc_start: 0.7803 (tp30) cc_final: 0.7544 (tm-30) REVERT: C 1010 GLN cc_start: 0.8362 (mt0) cc_final: 0.8136 (mm-40) REVERT: C 1050 MET cc_start: 0.8957 (mtp) cc_final: 0.8751 (mtp) outliers start: 45 outliers final: 33 residues processed: 210 average time/residue: 0.4658 time to fit residues: 118.7028 Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 261 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.187607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120118 restraints weight = 28633.634| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3174 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24435 Z= 0.107 Angle : 0.529 9.345 33312 Z= 0.272 Chirality : 0.044 0.297 3876 Planarity : 0.004 0.059 4251 Dihedral : 4.293 27.382 3201 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.75 % Allowed : 13.50 % Favored : 84.74 % 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: 0.68 (0.16), residues: 2955 helix: 2.29 (0.21), residues: 627 sheet: 0.47 (0.19), residues: 705 loop : -0.26 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.021 0.001 TYR B 170 PHE 0.015 0.001 PHE A 643 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (24366) covalent geometry : angle 0.51157 / 0.27 (33144) SS BOND : bond 0.00440 / 0.31 ( 39) SS BOND : angle 1.85973 / 1.18 ( 78) hydrogen bonds : bond 0.03658 / 2.37 ( 1058) hydrogen bonds : angle 5.43056 / 3.73 ( 2907) link_NAG-ASN : bond 0.00320 / 0.25 ( 30) link_NAG-ASN : angle 2.05038 / 1.49 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8686.91 seconds wall clock time: 148 minutes 43.13 seconds (8923.13 seconds total)