Starting phenix.real_space_refine on Sat Jul 4 21:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwv_23558/07_2026/7lwv_23558.cif" } resolution = 3.12 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= 0.097 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 101 5.16 5 C 15055 2.51 5 N 3879 2.21 5 O 4526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 23561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7694 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7710 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7681 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 4.84, per 1000 atoms: 0.21 Number of scatterers: 23561 At special positions: 0 Unit cell: (128.28, 135.763, 194.558, 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 101 16.00 O 4526 8.00 N 3879 7.00 C 15055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 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 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.02 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 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 234 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 26.8% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.572A 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 389 removed outlier: 4.669A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.878A 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 616 through 620 removed outlier: 4.315A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.810A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.989A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.830A 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: 3.684A 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 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.536A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.257A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.237A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.955A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.799A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.861A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 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: 3.501A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.044A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.548A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.108A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.141A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.406A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.747A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.836A 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: 4.851A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.619A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 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: 3.883A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.843A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.513A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.520A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.538A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.521A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.817A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.898A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.763A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.772A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.817A 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: 3.864A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.405A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.414A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.735A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.705A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.088A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.739A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 728 removed outlier: 6.127A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.649A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.807A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.862A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.952A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.631A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.424A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.787A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.245A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.827A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.456A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.650A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.511A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.455A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.661A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 2.42 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: 6227 1.33 - 1.46: 4529 1.46 - 1.58: 13194 1.58 - 1.70: 0 1.70 - 1.83: 125 Bond restraints: 24075 Sorted by residual: bond pdb=" C5 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 24070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 26463 2.33 - 4.65: 6015 4.65 - 6.98: 270 6.98 - 9.30: 11 9.30 - 11.63: 4 Bond angle restraints: 32763 Sorted by residual: angle pdb=" CA ASP C 570 " pdb=" CB ASP C 570 " pdb=" CG ASP C 570 " ideal model delta sigma weight residual 112.60 121.02 -8.42 1.00e+00 1.00e+00 7.10e+01 angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.17 6.43 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.03 -6.43 1.00e+00 1.00e+00 4.14e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 32758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 13101 17.68 - 35.37: 740 35.37 - 53.05: 111 53.05 - 70.73: 42 70.73 - 88.42: 25 Dihedral angle restraints: 14019 sinusoidal: 5359 harmonic: 8660 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 -168.55 82.55 1 1.00e+01 1.00e-02 8.36e+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 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+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 -161.02 75.02 1 1.00e+01 1.00e-02 7.12e+01 ... (remaining 14016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 3835 0.274 - 0.549: 25 0.549 - 0.823: 0 0.823 - 1.098: 0 1.098 - 1.372: 3 Chirality restraints: 3863 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.71e+01 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 ... (remaining 3860 not shown) Planarity restraints: 4211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.228 2.00e-02 2.50e+03 1.20e-01 3.58e+02 pdb=" CG TRP C 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.096 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.163 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.149 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " -0.133 2.00e-02 2.50e+03 1.43e-01 2.54e+02 pdb=" CG ASN C 282 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.094 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" CG ASN A 234 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.158 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.123 2.00e-02 2.50e+03 ... (remaining 4208 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11052 2.99 - 3.47: 21962 3.47 - 3.94: 38354 3.94 - 4.42: 42515 4.42 - 4.90: 73386 Nonbonded interactions: 187269 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.525 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 3.040 nonbonded pdb=" OG SER A 975 " pdb=" OD2 ASP C 571 " model vdw 2.531 3.040 ... (remaining 187264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 o \ r (resid 867 through 868 and (name N or name CA or name C or name O or name CB ) \ ) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and ( \ name N or name CA or name C or name O or name CB )) or resid 1147 through 1310)) \ selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 479 or (resid 480 and (name N or name CA or name C or n \ ame O or name CB )) or resid 481 through 483 or resid 485 through 487 or (resid \ 488 and (name N or name CA or name C or name O or name CB )) or resid 489 throug \ h 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 through 582 or (resid 583 and (name N or name CA or name C or name O o \ r name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or na \ me C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 676 or resid 6 \ 90 through 744 or (resid 745 and (name N or name CA or name C or name O or name \ CB )) or resid 746 through 747 or (resid 748 and (name N or name CA or name C or \ name O or name CB )) or resid 749 through 810 or (resid 811 and (name N or name \ CA or name C or name O or name CB )) or resid 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 827 or resid 855 \ through 866 or (resid 867 through 868 and (name N or name CA or name C or name O \ or name CB )) or resid 869 through 1091 or (resid 1092 and (name N or name CA o \ r name C or name O or name CB )) or resid 1093 through 1143 or (resid 1144 throu \ gh 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147 t \ hrough 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 483 or resid 485 through 487 or (resid 488 and ( \ name N or name CA or name C or name O or name CB )) or resid 489 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 \ through 567 or (resid 568 and (name N or name CA or name C or name O or name CB \ )) or resid 569 through 582 or (resid 583 and (name N or name CA or name C or n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N o \ r name CA or name C or name O or name CB )) or resid 1147 through 1310)) } 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: 1.850 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.740 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.076 24146 Z= 0.769 Angle : 1.799 11.629 32939 Z= 1.201 Chirality : 0.101 1.372 3863 Planarity : 0.013 0.133 4177 Dihedral : 12.572 88.418 8332 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.82 % Favored : 94.87 % Rotamer: Outliers : 0.63 % Allowed : 2.20 % Favored : 97.17 % Cbeta Deviations : 0.14 % 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: -0.77 (0.14), residues: 2924 helix: -0.94 (0.17), residues: 674 sheet: 0.68 (0.21), residues: 544 loop : -0.69 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1019 TYR 0.128 0.019 TYR B 279 PHE 0.067 0.012 PHE B 718 TRP 0.228 0.026 TRP C 886 HIS 0.014 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.77 (24075) covalent geometry : angle 1.78174 / 1.20 (32763) SS BOND : bond 0.01453 / 0.81 ( 37) SS BOND : angle 2.14992 / 1.43 ( 74) hydrogen bonds : bond 0.16885 / 11.33 ( 1014) hydrogen bonds : angle 8.19848 / 5.67 ( 2793) link_NAG-ASN : bond 0.01427 / 0.88 ( 34) link_NAG-ASN : angle 4.69264 / 3.13 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 350 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8581 (m) cc_final: 0.8278 (p) REVERT: A 427 ASP cc_start: 0.6931 (m-30) cc_final: 0.6701 (m-30) REVERT: A 451 TYR cc_start: 0.7483 (m-80) cc_final: 0.7219 (m-10) REVERT: A 776 LYS cc_start: 0.8567 (tttt) cc_final: 0.8361 (tttm) REVERT: A 1125 ASN cc_start: 0.7250 (p0) cc_final: 0.7011 (p0) REVERT: B 100 ILE cc_start: 0.8876 (mt) cc_final: 0.8619 (mt) REVERT: B 740 MET cc_start: 0.8195 (tpt) cc_final: 0.7249 (tpt) REVERT: B 1050 MET cc_start: 0.8811 (ptp) cc_final: 0.8414 (ptp) REVERT: C 28 TYR cc_start: 0.7994 (m-80) cc_final: 0.7781 (m-80) REVERT: C 1144 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7580 (mt-10) outliers start: 16 outliers final: 7 residues processed: 365 average time/residue: 0.1547 time to fit residues: 87.8591 Evaluate side-chains 201 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 343 ASN A 370 ASN A 394 ASN A 675 GLN A 856 ASN A1010 GLN B 370 ASN B 764 ASN C 188 ASN C 360 ASN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145307 restraints weight = 28373.170| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.30 r_work: 0.3240 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24146 Z= 0.132 Angle : 0.628 10.681 32939 Z= 0.328 Chirality : 0.046 0.454 3863 Planarity : 0.004 0.052 4177 Dihedral : 5.693 50.576 3186 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.02 % Allowed : 5.66 % Favored : 93.31 % 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: 0.39 (0.15), residues: 2924 helix: 1.61 (0.20), residues: 657 sheet: 0.67 (0.19), residues: 701 loop : -0.50 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.020 0.001 TYR A 369 PHE 0.025 0.001 PHE C 565 TRP 0.013 0.002 TRP B 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (24075) covalent geometry : angle 0.60420 / 0.32 (32763) SS BOND : bond 0.00312 / 0.19 ( 37) SS BOND : angle 1.64357 / 1.07 ( 74) hydrogen bonds : bond 0.04835 / 3.14 ( 1014) hydrogen bonds : angle 5.99047 / 4.21 ( 2793) link_NAG-ASN : bond 0.00746 / 0.40 ( 34) link_NAG-ASN : angle 2.82154 / 1.91 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7202 (m-70) REVERT: A 307 THR cc_start: 0.8673 (m) cc_final: 0.8399 (p) REVERT: A 364 ASP cc_start: 0.7104 (t0) cc_final: 0.6872 (t0) REVERT: A 427 ASP cc_start: 0.7302 (m-30) cc_final: 0.7030 (m-30) REVERT: A 776 LYS cc_start: 0.9112 (tttt) cc_final: 0.8814 (tttm) REVERT: A 856 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.6113 (m-40) REVERT: B 697 MET cc_start: 0.8875 (ptp) cc_final: 0.8501 (ptm) REVERT: C 32 PHE cc_start: 0.8492 (m-10) cc_final: 0.8199 (m-10) REVERT: C 105 ILE cc_start: 0.8386 (mt) cc_final: 0.8164 (mt) REVERT: C 118 LEU cc_start: 0.7822 (tp) cc_final: 0.7298 (mt) REVERT: C 237 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8125 (mtp85) REVERT: C 886 TRP cc_start: 0.7533 (p90) cc_final: 0.7292 (p90) outliers start: 26 outliers final: 12 residues processed: 240 average time/residue: 0.1500 time to fit residues: 57.6272 Evaluate side-chains 179 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 39 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 ASN A1010 GLN A1088 HIS A1125 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 188 ASN C 207 HIS C1048 HIS C1088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140204 restraints weight = 28359.623| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.36 r_work: 0.3161 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24146 Z= 0.184 Angle : 0.609 11.057 32939 Z= 0.316 Chirality : 0.047 0.404 3863 Planarity : 0.004 0.043 4177 Dihedral : 5.125 54.059 3181 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 1.30 % Allowed : 7.94 % Favored : 90.76 % 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: 0.42 (0.15), residues: 2924 helix: 1.78 (0.21), residues: 662 sheet: 0.62 (0.18), residues: 702 loop : -0.53 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.020 0.002 TYR C1067 PHE 0.023 0.002 PHE C 565 TRP 0.012 0.002 TRP C 886 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (24075) covalent geometry : angle 0.58736 / 0.31 (32763) SS BOND : bond 0.00364 / 0.23 ( 37) SS BOND : angle 1.80850 / 1.11 ( 74) hydrogen bonds : bond 0.04974 / 3.26 ( 1014) hydrogen bonds : angle 5.76310 / 4.04 ( 2793) link_NAG-ASN : bond 0.00452 / 0.24 ( 34) link_NAG-ASN : angle 2.57665 / 1.77 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8665 (m-10) cc_final: 0.8443 (m-80) REVERT: A 427 ASP cc_start: 0.7343 (m-30) cc_final: 0.7089 (m-30) REVERT: A 776 LYS cc_start: 0.9101 (tttt) cc_final: 0.8794 (tttm) REVERT: B 190 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7941 (mtt90) REVERT: B 1119 ASN cc_start: 0.7929 (m110) cc_final: 0.7679 (m-40) REVERT: C 32 PHE cc_start: 0.8584 (m-10) cc_final: 0.8253 (m-10) REVERT: C 359 SER cc_start: 0.8746 (p) cc_final: 0.8529 (t) outliers start: 33 outliers final: 24 residues processed: 209 average time/residue: 0.1563 time to fit residues: 53.5207 Evaluate side-chains 185 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 146 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN A1048 HIS A1125 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.167221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138089 restraints weight = 28412.958| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.33 r_work: 0.3144 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 24146 Z= 0.240 Angle : 0.629 11.374 32939 Z= 0.325 Chirality : 0.048 0.374 3863 Planarity : 0.004 0.044 4177 Dihedral : 5.096 57.497 3181 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 8.73 % Favored : 89.54 % 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: 0.17 (0.15), residues: 2924 helix: 1.61 (0.21), residues: 661 sheet: 0.44 (0.18), residues: 720 loop : -0.70 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.020 0.002 TYR A1067 PHE 0.028 0.002 PHE C 565 TRP 0.012 0.002 TRP C 886 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (24075) covalent geometry : angle 0.60905 / 0.32 (32763) SS BOND : bond 0.00519 / 0.35 ( 37) SS BOND : angle 1.85218 / 1.13 ( 74) hydrogen bonds : bond 0.05208 / 3.44 ( 1014) hydrogen bonds : angle 5.78747 / 4.05 ( 2793) link_NAG-ASN : bond 0.00388 / 0.21 ( 34) link_NAG-ASN : angle 2.49686 / 1.70 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8664 (m-10) cc_final: 0.8401 (m-80) REVERT: A 501 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: A 747 THR cc_start: 0.8895 (m) cc_final: 0.8690 (p) REVERT: A 776 LYS cc_start: 0.9069 (tttt) cc_final: 0.8779 (tttm) REVERT: A 904 TYR cc_start: 0.7635 (m-10) cc_final: 0.7395 (m-10) REVERT: B 190 ARG cc_start: 0.8276 (mtt180) cc_final: 0.8002 (mtt90) REVERT: B 233 ILE cc_start: 0.7724 (tt) cc_final: 0.7252 (pt) REVERT: C 105 ILE cc_start: 0.8405 (mt) cc_final: 0.8192 (mt) REVERT: C 118 LEU cc_start: 0.7985 (tp) cc_final: 0.7498 (mp) REVERT: C 359 SER cc_start: 0.8779 (p) cc_final: 0.8529 (t) outliers start: 44 outliers final: 33 residues processed: 207 average time/residue: 0.1514 time to fit residues: 51.5718 Evaluate side-chains 191 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144916 restraints weight = 28152.574| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.19 r_work: 0.3252 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24146 Z= 0.116 Angle : 0.526 9.703 32939 Z= 0.271 Chirality : 0.044 0.363 3863 Planarity : 0.004 0.039 4177 Dihedral : 4.632 56.364 3181 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 0.98 % Allowed : 10.03 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2924 helix: 2.12 (0.21), residues: 654 sheet: 0.45 (0.18), residues: 728 loop : -0.55 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.019 0.001 TYR A1067 PHE 0.027 0.001 PHE C 565 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24075) covalent geometry : angle 0.50697 / 0.27 (32763) SS BOND : bond 0.00305 / 0.21 ( 37) SS BOND : angle 1.48312 / 0.88 ( 74) hydrogen bonds : bond 0.04025 / 2.63 ( 1014) hydrogen bonds : angle 5.43165 / 3.81 ( 2793) link_NAG-ASN : bond 0.00384 / 0.21 ( 34) link_NAG-ASN : angle 2.24749 / 1.53 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.875 Fit side-chains REVERT: A 269 TYR cc_start: 0.8685 (m-10) cc_final: 0.8336 (m-80) REVERT: A 501 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5576 (m-80) REVERT: A 776 LYS cc_start: 0.9085 (tttt) cc_final: 0.8694 (tttm) REVERT: A 904 TYR cc_start: 0.7517 (m-10) cc_final: 0.7289 (m-10) REVERT: B 190 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7878 (mtt90) REVERT: B 1119 ASN cc_start: 0.8029 (m110) cc_final: 0.7744 (m-40) REVERT: C 32 PHE cc_start: 0.8680 (m-10) cc_final: 0.8437 (m-10) REVERT: C 53 ASP cc_start: 0.7697 (m-30) cc_final: 0.7266 (m-30) REVERT: C 105 ILE cc_start: 0.8413 (mt) cc_final: 0.8171 (mt) REVERT: C 118 LEU cc_start: 0.7937 (tp) cc_final: 0.7604 (mp) REVERT: C 237 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8171 (mtp85) REVERT: C 886 TRP cc_start: 0.7738 (p90) cc_final: 0.7187 (p90) outliers start: 25 outliers final: 17 residues processed: 204 average time/residue: 0.1398 time to fit residues: 47.6995 Evaluate side-chains 184 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 131 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 188 ASN C 207 HIS C 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.171941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144482 restraints weight = 28406.602| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.27 r_work: 0.3230 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24146 Z= 0.118 Angle : 0.523 10.175 32939 Z= 0.267 Chirality : 0.044 0.356 3863 Planarity : 0.003 0.039 4177 Dihedral : 4.467 55.720 3181 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2924 helix: 2.20 (0.21), residues: 659 sheet: 0.53 (0.18), residues: 729 loop : -0.48 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.018 0.001 TYR A1067 PHE 0.025 0.001 PHE C 565 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24075) covalent geometry : angle 0.50613 / 0.26 (32763) SS BOND : bond 0.00346 / 0.24 ( 37) SS BOND : angle 1.41916 / 0.84 ( 74) hydrogen bonds : bond 0.03969 / 2.60 ( 1014) hydrogen bonds : angle 5.31810 / 3.73 ( 2793) link_NAG-ASN : bond 0.00366 / 0.19 ( 34) link_NAG-ASN : angle 2.16908 / 1.48 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8629 (m-10) cc_final: 0.8111 (m-10) REVERT: A 776 LYS cc_start: 0.8950 (tttt) cc_final: 0.8685 (tttm) REVERT: A 855 PHE cc_start: 0.6346 (m-80) cc_final: 0.5984 (m-80) REVERT: A 856 ASN cc_start: 0.7690 (p0) cc_final: 0.7454 (p0) REVERT: B 190 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7938 (mtt90) REVERT: B 1119 ASN cc_start: 0.8086 (m110) cc_final: 0.7813 (m-40) REVERT: C 118 LEU cc_start: 0.7942 (tp) cc_final: 0.7589 (mp) REVERT: C 886 TRP cc_start: 0.7806 (p90) cc_final: 0.7335 (p90) outliers start: 34 outliers final: 23 residues processed: 204 average time/residue: 0.1421 time to fit residues: 48.3717 Evaluate side-chains 187 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 211 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 260 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 269 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1106 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.171689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143117 restraints weight = 28151.084| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.32 r_work: 0.3216 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24146 Z= 0.129 Angle : 0.522 9.487 32939 Z= 0.267 Chirality : 0.044 0.350 3863 Planarity : 0.003 0.038 4177 Dihedral : 4.363 55.521 3180 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 1.49 % Allowed : 10.34 % Favored : 88.16 % 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: 0.59 (0.15), residues: 2924 helix: 2.22 (0.21), residues: 663 sheet: 0.49 (0.18), residues: 732 loop : -0.46 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.023 0.001 PHE C 565 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (24075) covalent geometry : angle 0.50522 / 0.26 (32763) SS BOND : bond 0.00309 / 0.21 ( 37) SS BOND : angle 1.54239 / 0.88 ( 74) hydrogen bonds : bond 0.04017 / 2.64 ( 1014) hydrogen bonds : angle 5.26656 / 3.68 ( 2793) link_NAG-ASN : bond 0.00360 / 0.19 ( 34) link_NAG-ASN : angle 2.10822 / 1.44 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8661 (m-10) cc_final: 0.8119 (m-10) REVERT: A 501 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5387 (m-80) REVERT: A 776 LYS cc_start: 0.8997 (tttt) cc_final: 0.8695 (tttm) REVERT: A 855 PHE cc_start: 0.6393 (m-80) cc_final: 0.5993 (m-80) REVERT: A 856 ASN cc_start: 0.7776 (p0) cc_final: 0.7534 (p0) REVERT: B 190 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7884 (mtt90) REVERT: B 1119 ASN cc_start: 0.8212 (m110) cc_final: 0.7898 (m-40) REVERT: C 886 TRP cc_start: 0.7874 (p90) cc_final: 0.7401 (p90) outliers start: 38 outliers final: 30 residues processed: 208 average time/residue: 0.1352 time to fit residues: 46.5279 Evaluate side-chains 197 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 99 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 228 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 252 optimal weight: 0.3980 chunk 290 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142488 restraints weight = 28209.321| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.31 r_work: 0.3218 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24146 Z= 0.131 Angle : 0.521 9.414 32939 Z= 0.267 Chirality : 0.044 0.348 3863 Planarity : 0.004 0.037 4177 Dihedral : 4.325 55.264 3180 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.69 % Allowed : 10.54 % Favored : 87.77 % 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: 0.62 (0.15), residues: 2924 helix: 2.24 (0.21), residues: 663 sheet: 0.53 (0.18), residues: 737 loop : -0.45 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.021 0.001 TYR A 904 PHE 0.022 0.001 PHE C 168 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (24075) covalent geometry : angle 0.50495 / 0.26 (32763) SS BOND : bond 0.00316 / 0.21 ( 37) SS BOND : angle 1.44736 / 0.85 ( 74) hydrogen bonds : bond 0.04003 / 2.63 ( 1014) hydrogen bonds : angle 5.23971 / 3.66 ( 2793) link_NAG-ASN : bond 0.00361 / 0.19 ( 34) link_NAG-ASN : angle 2.08581 / 1.43 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7130 (m-70) REVERT: A 269 TYR cc_start: 0.8632 (m-10) cc_final: 0.8086 (m-10) REVERT: A 501 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: A 776 LYS cc_start: 0.8925 (tttt) cc_final: 0.8680 (tttm) REVERT: A 855 PHE cc_start: 0.6336 (m-80) cc_final: 0.5964 (m-80) REVERT: A 856 ASN cc_start: 0.7716 (p0) cc_final: 0.7477 (p0) REVERT: A 904 TYR cc_start: 0.7605 (m-10) cc_final: 0.7253 (m-10) REVERT: B 190 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7898 (mtt90) REVERT: B 1119 ASN cc_start: 0.8233 (m110) cc_final: 0.7891 (m-40) REVERT: C 53 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: C 408 ARG cc_start: 0.6963 (ptm-80) cc_final: 0.6660 (tmm160) REVERT: C 886 TRP cc_start: 0.7782 (p90) cc_final: 0.7399 (p90) outliers start: 43 outliers final: 37 residues processed: 208 average time/residue: 0.1429 time to fit residues: 49.7712 Evaluate side-chains 209 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144023 restraints weight = 28195.450| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.37 r_work: 0.3226 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24146 Z= 0.108 Angle : 0.505 9.823 32939 Z= 0.258 Chirality : 0.044 0.344 3863 Planarity : 0.003 0.037 4177 Dihedral : 4.171 54.958 3180 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.57 % Allowed : 10.70 % Favored : 87.73 % 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: 0.70 (0.16), residues: 2924 helix: 2.26 (0.21), residues: 675 sheet: 0.55 (0.19), residues: 724 loop : -0.38 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.019 0.001 TYR B 170 PHE 0.023 0.001 PHE C 168 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24075) covalent geometry : angle 0.48896 / 0.25 (32763) SS BOND : bond 0.00287 / 0.19 ( 37) SS BOND : angle 1.48370 / 0.80 ( 74) hydrogen bonds : bond 0.03672 / 2.40 ( 1014) hydrogen bonds : angle 5.11911 / 3.58 ( 2793) link_NAG-ASN : bond 0.00362 / 0.20 ( 34) link_NAG-ASN : angle 2.00516 / 1.37 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.7049 (m-70) REVERT: A 269 TYR cc_start: 0.8661 (m-10) cc_final: 0.8261 (m-10) REVERT: A 776 LYS cc_start: 0.9048 (tttt) cc_final: 0.8693 (tttm) REVERT: A 855 PHE cc_start: 0.6384 (m-80) cc_final: 0.6000 (m-80) REVERT: A 856 ASN cc_start: 0.7784 (p0) cc_final: 0.7566 (p0) REVERT: A 904 TYR cc_start: 0.7794 (m-10) cc_final: 0.7505 (m-10) REVERT: B 170 TYR cc_start: 0.7745 (t80) cc_final: 0.7533 (t80) REVERT: B 190 ARG cc_start: 0.8278 (mtt180) cc_final: 0.8017 (mtt90) REVERT: B 1119 ASN cc_start: 0.8162 (m110) cc_final: 0.7823 (m-40) REVERT: C 408 ARG cc_start: 0.6990 (ptm-80) cc_final: 0.6689 (tmm160) REVERT: C 675 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: C 886 TRP cc_start: 0.7840 (p90) cc_final: 0.7406 (p90) outliers start: 40 outliers final: 34 residues processed: 213 average time/residue: 0.1291 time to fit residues: 45.9621 Evaluate side-chains 205 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 110 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 212 optimal weight: 0.0570 chunk 188 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 901 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.173050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144327 restraints weight = 28191.139| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.38 r_work: 0.3224 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24146 Z= 0.103 Angle : 0.497 9.575 32939 Z= 0.253 Chirality : 0.043 0.342 3863 Planarity : 0.003 0.035 4177 Dihedral : 4.074 54.694 3180 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.42 % Allowed : 10.97 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.16), residues: 2924 helix: 2.38 (0.21), residues: 670 sheet: 0.57 (0.19), residues: 725 loop : -0.33 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.018 0.001 TYR C 170 PHE 0.023 0.001 PHE C 168 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (24075) covalent geometry : angle 0.48137 / 0.25 (32763) SS BOND : bond 0.00294 / 0.20 ( 37) SS BOND : angle 1.45407 / 0.82 ( 74) hydrogen bonds : bond 0.03584 / 2.34 ( 1014) hydrogen bonds : angle 5.05181 / 3.53 ( 2793) link_NAG-ASN : bond 0.00361 / 0.19 ( 34) link_NAG-ASN : angle 1.94338 / 1.34 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.7089 (m-70) REVERT: A 501 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: A 776 LYS cc_start: 0.8987 (tttt) cc_final: 0.8696 (tttm) REVERT: A 825 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7704 (mmtm) REVERT: A 855 PHE cc_start: 0.6237 (m-80) cc_final: 0.5874 (m-80) REVERT: A 856 ASN cc_start: 0.7632 (p0) cc_final: 0.7414 (p0) REVERT: A 904 TYR cc_start: 0.7814 (m-10) cc_final: 0.7611 (m-10) REVERT: B 190 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7914 (mtt90) REVERT: B 1119 ASN cc_start: 0.8076 (m110) cc_final: 0.7747 (m-40) REVERT: C 53 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: C 380 TYR cc_start: 0.8259 (m-10) cc_final: 0.7858 (m-80) REVERT: C 408 ARG cc_start: 0.6938 (ptm-80) cc_final: 0.6592 (tmm160) REVERT: C 886 TRP cc_start: 0.7857 (p90) cc_final: 0.7490 (p90) outliers start: 36 outliers final: 32 residues processed: 201 average time/residue: 0.1441 time to fit residues: 48.3086 Evaluate side-chains 205 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 233 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 220 optimal weight: 0.0770 chunk 168 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 236 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145607 restraints weight = 28285.216| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.34 r_work: 0.3251 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24146 Z= 0.094 Angle : 0.489 9.606 32939 Z= 0.249 Chirality : 0.043 0.342 3863 Planarity : 0.003 0.039 4177 Dihedral : 3.986 54.587 3180 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.42 % Allowed : 11.17 % Favored : 87.42 % 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: 0.85 (0.16), residues: 2924 helix: 2.47 (0.21), residues: 671 sheet: 0.59 (0.19), residues: 713 loop : -0.28 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.017 0.001 TYR C1067 PHE 0.023 0.001 PHE C 168 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (24075) covalent geometry : angle 0.47506 / 0.25 (32763) SS BOND : bond 0.00273 / 0.19 ( 37) SS BOND : angle 1.28708 / 0.74 ( 74) hydrogen bonds : bond 0.03397 / 2.22 ( 1014) hydrogen bonds : angle 4.96257 / 3.47 ( 2793) link_NAG-ASN : bond 0.00364 / 0.20 ( 34) link_NAG-ASN : angle 1.87624 / 1.30 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5584.65 seconds wall clock time: 96 minutes 24.12 seconds (5784.12 seconds total)