Starting phenix.real_space_refine on Sat Mar 7 15:12:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z97_11119/03_2026/6z97_11119.map" } resolution = 3.4 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= 0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 14973 2.51 5 N 3836 2.21 5 O 4554 1.98 5 H 21895 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45362 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 14982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 14982 Classifications: {'peptide': 995} Link IDs: {'PTRANS': 49, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 14831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 14831 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 49, 'TRANS': 939} Chain breaks: 9 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 14863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 14863 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.35, per 1000 atoms: 0.18 Number of scatterers: 45362 At special positions: 0 Unit cell: (123.67, 136.95, 193.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 4554 8.00 N 3836 7.00 C 14973 6.00 H 21895 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1314 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 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: 75 helices and 46 sheets defined 27.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 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 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.738A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.307A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.687A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.871A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.793A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.291A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.923A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.691A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.342A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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: 3.559A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.084A 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 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.324A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 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 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.383A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.411A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.123A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.718A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.748A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.696A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.419A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.531A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.848A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.716A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.898A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.876A 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: 4.471A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.058A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.566A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.110A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 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: 6.348A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 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 565 through 566 removed outlier: 6.895A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.474A 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: 3.863A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.308A 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: 6.910A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.828A 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: 4.489A 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: 4.268A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.257A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.766A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.199A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.831A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.442A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.895A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.409A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2781 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: 11.21 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 21893 1.04 - 1.23: 1342 1.23 - 1.43: 8931 1.43 - 1.63: 13583 1.63 - 1.83: 128 Bond restraints: 45877 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG B1313 " pdb=" O5 NAG B1313 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 45872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 80459 1.51 - 3.02: 1618 3.02 - 4.53: 156 4.53 - 6.04: 20 6.04 - 7.55: 3 Bond angle restraints: 82256 Sorted by residual: angle pdb=" N SER B 813 " pdb=" CA SER B 813 " pdb=" C SER B 813 " ideal model delta sigma weight residual 110.80 117.40 -6.60 2.13e+00 2.20e-01 9.61e+00 angle pdb=" C PRO B 812 " pdb=" N SER B 813 " pdb=" CA SER B 813 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CG ASN A 343 " pdb=" ND2 ASN A 343 " pdb="HD21 ASN A 343 " ideal model delta sigma weight residual 120.00 127.55 -7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 ... (remaining 82251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 21147 17.81 - 35.63: 1202 35.63 - 53.44: 377 53.44 - 71.26: 93 71.26 - 89.07: 23 Dihedral angle restraints: 22842 sinusoidal: 12481 harmonic: 10361 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.88 79.88 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.69 77.69 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -160.88 74.88 1 1.00e+01 1.00e-02 7.10e+01 ... (remaining 22839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3844 0.119 - 0.238: 77 0.238 - 0.357: 3 0.357 - 0.476: 1 0.476 - 0.594: 2 Chirality restraints: 3927 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 3924 not shown) Planarity restraints: 6999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 122 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ASN A 122 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN A 122 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 123 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.024 2.00e-02 2.50e+03 2.11e-02 6.70e+00 pdb=" CG ASN B 61 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.032 2.00e-02 2.50e+03 pdb="HD21 ASN B 61 " -0.006 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ASN C 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.014 2.00e-02 2.50e+03 ... (remaining 6996 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 775 2.09 - 2.72: 75654 2.72 - 3.35: 126457 3.35 - 3.97: 166633 3.97 - 4.60: 259870 Nonbonded interactions: 629389 Sorted by model distance: nonbonded pdb=" H THR C 716 " pdb=" O GLN C1071 " model vdw 1.468 2.450 nonbonded pdb=" O PRO C1053 " pdb="HE21 GLN C1054 " model vdw 1.487 2.450 nonbonded pdb=" O LYS B 811 " pdb=" H SER B 813 " model vdw 1.505 2.450 nonbonded pdb=" H THR A 716 " pdb=" O GLN A1071 " model vdw 1.516 2.450 nonbonded pdb="HD21 ASN C 334 " pdb=" O ASN C 360 " model vdw 1.560 2.450 ... (remaining 629384 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 45 or (resid \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 52 or (resid 53 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 54 through 60 or (resid 61 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 \ or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 62 through \ 66 or resid 82 through 87 or (resid 88 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 89 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 116 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 126 through 131 or (resid 132 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 13 \ 3 or (resid 134 through 138 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 139 through 140 or resid 166 through 168 or ( \ resid 169 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 170 through 171 or (resid 172 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 188 through 196 or (resid \ 200 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or name HB \ 2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH )) or r \ esid 201 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or (resid 215 and (name N or name CA or name C \ or name O or name CB or name HA )) or resid 216 through 217 or (resid 218 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 219 through 223 or (resid 224 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 225 through 263 or resid 265 through 308 o \ r (resid 309 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 310 through 323 or (resid 324 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 325 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 334 through 457 or (resid 458 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 459 through 528 or (resid 529 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 530 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 538 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 749 through 793 or (resid 794 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 795 or (resid 796 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 797 through 827 \ or (resid 854 and (name N or name CA or name C or name O or name CB or name HA ) \ ) or (resid 855 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 856 through 867 or (resid 868 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 869 through 939 or ( \ resid 940 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 986 through 987 or (resid \ 988 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 989 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 1143 through 1144 or (resid 11 \ 45 through 1146 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 1147 through 1314)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 45 or (resid \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 66 or resid 82 through 87 or (resid 88 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 89 through 10 \ 9 or (resid 110 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 111 or (resid 112 through 113 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or (resid 116 and (name N or \ name CA or name C or name O or name CB or name OG or name HA or name HB2 or name \ HB3 or name HG )) or resid 117 through 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 130 through 134 \ or (resid 135 through 138 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 139 through 140 or (resid 166 and (name N or n \ ame CA or name C or name O or name CB or name SG or name HA or name HB2 or name \ HB3)) or resid 167 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 192 through 195 or (resid 19 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 200 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 207 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 238 through 241 or (resid 242 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 263 or resid 265 through 280 or (resid 2 \ 81 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 282 through 297 or (resid 298 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 299 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 325 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 390 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 45 \ 9 through 567 or (resid 568 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 569 through 570 or (resid 571 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 572 thro \ ugh 579 or (resid 580 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 581 or (resid 582 through 583 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 584 through 61 \ 3 or (resid 614 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 615 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 620 through 676 or ( \ resid 690 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HE21 or name HE22)) or resid 691 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 746 through 827 or (resid 854 and (name N or name CA or name C or name O or n \ ame CB or name HA )) or (resid 855 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 856 through 867 or (resid 868 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 8 \ 69 through 939 or (resid 940 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 941 through 984 or (resid 985 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 986 thr \ ough 987 or (resid 988 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 989 through 1063 or (resid 1064 and (name N or nam \ e CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name C \ E1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name \ HD2 or name HE1)) or resid 1065 through 1143 or (resid 1144 through 1146 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 1147 through 1308)) 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 name H or name HA )) or resid 54 through 66 or resid 8 \ 2 through 95 or (resid 96 through 97 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 98 through 113 or (resid 116 and (na \ me N or name CA or name C or name O or name CB or name OG or name HA or name HB2 \ or name HB3 or name HG )) or resid 117 through 134 or (resid 135 through 138 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 139 through 140 or (resid 166 and (name N or name CA or name C or name O or \ name CB or name SG or name HA or name HB2 or name HB3)) or resid 167 through 17 \ 2 or (resid 188 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 189 through 195 or (resid 196 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or (resid 200 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or \ name HD2 or name HE1 or name HE2 or name HH )) or resid 201 through 205 or (resi \ d 206 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 207 through 209 or (resid 210 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or (resid 215 and (name N or name CA or \ name C or name O or name CB or name HA )) or resid 216 through 217 or (resid 21 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 219 through 223 or (resid 224 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 225 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 235 th \ rough 236 or (resid 237 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 238 through 297 or (resid 298 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 299 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 310 through 332 or (resid 333 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 334 through 342 or \ (resid 343 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) \ or resid 344 through 388 or (resid 389 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 390 through 527 or (resid 528 thr \ ough 529 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 530 through 536 or (resid 537 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 538 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 555 through 557 or (resid 558 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 559 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 569 through 570 or (resid 571 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 572 through 579 or (resid 580 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 58 \ 1 or (resid 582 through 583 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 584 through 602 or (resid 603 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or nam \ e H or name HA or name HB2 or name HB3 or name HD21)) or resid 604 through 618 o \ r (resid 619 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 620 through 645 or (resid 646 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 647 through 795 or (res \ id 796 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 797 through 1063 or (resid 1064 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1) \ ) or resid 1065 through 1141 or (resid 1142 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 1143 or (resid 1144 through 1 \ 146 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 1147 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 12.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 42.230 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24070 Z= 0.201 Angle : 0.677 22.012 32924 Z= 0.339 Chirality : 0.049 0.594 3927 Planarity : 0.004 0.047 4159 Dihedral : 12.078 89.072 9156 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.73 % Allowed : 5.28 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2921 helix: 0.41 (0.20), residues: 698 sheet: -0.22 (0.19), residues: 662 loop : -1.02 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1019 TYR 0.018 0.001 TYR A 369 PHE 0.016 0.001 PHE B 86 TRP 0.007 0.001 TRP A1102 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00424 (23982) covalent geometry : angle 0.61169 (32699) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.20196 ( 78) hydrogen bonds : bond 0.09291 ( 1024) hydrogen bonds : angle 7.10495 ( 2781) link_BETA1-4 : bond 0.00187 ( 11) link_BETA1-4 : angle 1.43466 ( 33) link_NAG-ASN : bond 0.00509 ( 38) link_NAG-ASN : angle 4.85509 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1111 GLU cc_start: 0.7350 (tt0) cc_final: 0.7119 (tt0) REVERT: B 92 PHE cc_start: 0.8036 (t80) cc_final: 0.7800 (t80) REVERT: B 878 LEU cc_start: 0.8965 (tp) cc_final: 0.8561 (mt) REVERT: C 269 TYR cc_start: 0.7028 (m-80) cc_final: 0.6662 (m-80) REVERT: C 374 PHE cc_start: 0.7107 (m-80) cc_final: 0.6897 (m-80) REVERT: C 389 ASP cc_start: 0.7134 (m-30) cc_final: 0.6796 (t0) REVERT: C 515 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7943 (p90) REVERT: C 983 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7122 (ttp-110) outliers start: 18 outliers final: 8 residues processed: 366 average time/residue: 0.3910 time to fit residues: 213.9679 Evaluate side-chains 228 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124056 restraints weight = 90441.056| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.28 r_work: 0.3139 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24070 Z= 0.253 Angle : 0.630 8.133 32924 Z= 0.331 Chirality : 0.047 0.340 3927 Planarity : 0.004 0.049 4159 Dihedral : 6.444 58.172 4209 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.45 % Allowed : 9.07 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 2921 helix: 0.86 (0.20), residues: 674 sheet: -0.52 (0.19), residues: 667 loop : -1.13 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 357 TYR 0.016 0.002 TYR C 380 PHE 0.022 0.002 PHE C 238 TRP 0.010 0.001 TRP A 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00585 (23982) covalent geometry : angle 0.60974 (32699) SS BOND : bond 0.00578 ( 39) SS BOND : angle 1.62060 ( 78) hydrogen bonds : bond 0.05234 ( 1024) hydrogen bonds : angle 5.99289 ( 2781) link_BETA1-4 : bond 0.00259 ( 11) link_BETA1-4 : angle 1.06120 ( 33) link_NAG-ASN : bond 0.00329 ( 38) link_NAG-ASN : angle 2.40576 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6182 (m-90) cc_final: 0.5583 (m-90) REVERT: A 988 GLU cc_start: 0.7804 (tp30) cc_final: 0.7569 (tp30) REVERT: A 1145 LEU cc_start: 0.7506 (mp) cc_final: 0.7126 (tt) REVERT: B 436 TRP cc_start: 0.6218 (p90) cc_final: 0.5999 (p90) REVERT: B 878 LEU cc_start: 0.9242 (tp) cc_final: 0.8936 (mt) REVERT: B 1072 GLU cc_start: 0.6964 (pt0) cc_final: 0.6741 (pt0) REVERT: C 269 TYR cc_start: 0.7656 (m-80) cc_final: 0.7071 (m-80) REVERT: C 378 LYS cc_start: 0.7436 (ttmm) cc_final: 0.7129 (ttpt) REVERT: C 515 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8118 (p90) outliers start: 36 outliers final: 22 residues processed: 272 average time/residue: 0.3441 time to fit residues: 148.7439 Evaluate side-chains 228 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 99 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127455 restraints weight = 90688.762| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.00 r_work: 0.3198 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24070 Z= 0.206 Angle : 0.578 7.741 32924 Z= 0.302 Chirality : 0.045 0.348 3927 Planarity : 0.004 0.044 4159 Dihedral : 6.026 57.867 4209 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.41 % Allowed : 10.04 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 2921 helix: 1.08 (0.21), residues: 676 sheet: -0.48 (0.19), residues: 664 loop : -1.15 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.014 0.001 TYR B 369 PHE 0.022 0.001 PHE C 374 TRP 0.007 0.001 TRP A1102 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00473 (23982) covalent geometry : angle 0.56092 (32699) SS BOND : bond 0.00566 ( 39) SS BOND : angle 1.61707 ( 78) hydrogen bonds : bond 0.04839 ( 1024) hydrogen bonds : angle 5.76208 ( 2781) link_BETA1-4 : bond 0.00216 ( 11) link_BETA1-4 : angle 1.09281 ( 33) link_NAG-ASN : bond 0.00276 ( 38) link_NAG-ASN : angle 2.00537 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 CYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4825 (t) REVERT: A 1145 LEU cc_start: 0.7397 (mp) cc_final: 0.7049 (tt) REVERT: B 878 LEU cc_start: 0.9227 (tp) cc_final: 0.8685 (mt) REVERT: B 1072 GLU cc_start: 0.6868 (pt0) cc_final: 0.6628 (pt0) REVERT: C 269 TYR cc_start: 0.7579 (m-80) cc_final: 0.6984 (m-80) REVERT: C 389 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6933 (t0) outliers start: 35 outliers final: 27 residues processed: 240 average time/residue: 0.3224 time to fit residues: 124.9331 Evaluate side-chains 226 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 274 optimal weight: 0.9990 chunk 129 optimal weight: 40.0000 chunk 235 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 290 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B1002 GLN C 907 ASN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 150)---------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121222 restraints weight = 90762.407| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.91 r_work: 0.3156 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24070 Z= 0.142 Angle : 0.537 6.608 32924 Z= 0.279 Chirality : 0.044 0.221 3927 Planarity : 0.004 0.045 4159 Dihedral : 5.713 58.541 4207 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.33 % Allowed : 10.24 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 2921 helix: 1.28 (0.21), residues: 684 sheet: -0.44 (0.19), residues: 669 loop : -1.09 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.022 0.001 TYR C 508 PHE 0.041 0.001 PHE A 456 TRP 0.007 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00326 (23982) covalent geometry : angle 0.52331 (32699) SS BOND : bond 0.00276 ( 39) SS BOND : angle 1.47381 ( 78) hydrogen bonds : bond 0.04381 ( 1024) hydrogen bonds : angle 5.52376 ( 2781) link_BETA1-4 : bond 0.00231 ( 11) link_BETA1-4 : angle 1.03972 ( 33) link_NAG-ASN : bond 0.00207 ( 38) link_NAG-ASN : angle 1.70745 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 LEU cc_start: 0.7667 (mp) cc_final: 0.7241 (tt) REVERT: B 878 LEU cc_start: 0.9260 (tp) cc_final: 0.8714 (mt) REVERT: B 907 ASN cc_start: 0.8783 (t0) cc_final: 0.8303 (t0) REVERT: C 269 TYR cc_start: 0.7626 (m-80) cc_final: 0.6973 (m-80) REVERT: C 389 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 572 THR cc_start: 0.8402 (p) cc_final: 0.8191 (t) outliers start: 33 outliers final: 27 residues processed: 234 average time/residue: 0.3359 time to fit residues: 126.2655 Evaluate side-chains 227 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 250 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126208 restraints weight = 90513.957| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.19 r_work: 0.3166 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24070 Z= 0.172 Angle : 0.538 6.473 32924 Z= 0.280 Chirality : 0.044 0.191 3927 Planarity : 0.004 0.045 4159 Dihedral : 5.593 58.722 4207 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.49 % Allowed : 10.48 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2921 helix: 1.39 (0.21), residues: 678 sheet: -0.41 (0.19), residues: 668 loop : -1.10 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1014 TYR 0.020 0.001 TYR C 508 PHE 0.043 0.001 PHE A 456 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00396 (23982) covalent geometry : angle 0.52520 (32699) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.36833 ( 78) hydrogen bonds : bond 0.04400 ( 1024) hydrogen bonds : angle 5.46574 ( 2781) link_BETA1-4 : bond 0.00240 ( 11) link_BETA1-4 : angle 1.01906 ( 33) link_NAG-ASN : bond 0.00198 ( 38) link_NAG-ASN : angle 1.66248 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 269 TYR cc_start: 0.7550 (m-80) cc_final: 0.6925 (m-80) REVERT: C 389 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7013 (t0) REVERT: C 568 ASP cc_start: 0.8000 (t70) cc_final: 0.7766 (t70) REVERT: C 572 THR cc_start: 0.8400 (p) cc_final: 0.8155 (t) outliers start: 37 outliers final: 29 residues processed: 233 average time/residue: 0.3086 time to fit residues: 116.3082 Evaluate side-chains 228 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 291 optimal weight: 0.3980 chunk 292 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 263 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126762 restraints weight = 90332.414| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.17 r_work: 0.3143 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24070 Z= 0.134 Angle : 0.518 7.670 32924 Z= 0.270 Chirality : 0.044 0.182 3927 Planarity : 0.004 0.046 4159 Dihedral : 5.357 59.267 4206 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.21 % Allowed : 11.05 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2921 helix: 1.47 (0.21), residues: 691 sheet: -0.33 (0.19), residues: 677 loop : -1.01 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.020 0.001 TYR C 508 PHE 0.035 0.001 PHE A 456 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00305 (23982) covalent geometry : angle 0.50785 (32699) SS BOND : bond 0.00221 ( 39) SS BOND : angle 1.28790 ( 78) hydrogen bonds : bond 0.04135 ( 1024) hydrogen bonds : angle 5.31969 ( 2781) link_BETA1-4 : bond 0.00240 ( 11) link_BETA1-4 : angle 0.98315 ( 33) link_NAG-ASN : bond 0.00173 ( 38) link_NAG-ASN : angle 1.49758 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 907 ASN cc_start: 0.8748 (t0) cc_final: 0.8268 (t0) REVERT: C 269 TYR cc_start: 0.7523 (m-80) cc_final: 0.6922 (m-80) REVERT: C 389 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7107 (t0) REVERT: C 421 TYR cc_start: 0.8312 (m-10) cc_final: 0.7315 (m-10) outliers start: 30 outliers final: 25 residues processed: 229 average time/residue: 0.2852 time to fit residues: 105.3564 Evaluate side-chains 220 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 79 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 152 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 chunk 293 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128740 restraints weight = 89874.891| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.08 r_work: 0.3215 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24070 Z= 0.124 Angle : 0.510 8.616 32924 Z= 0.263 Chirality : 0.043 0.164 3927 Planarity : 0.003 0.044 4159 Dihedral : 5.152 59.500 4206 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.09 % Allowed : 11.41 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2921 helix: 1.57 (0.21), residues: 696 sheet: -0.23 (0.19), residues: 670 loop : -0.96 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.023 0.001 TYR A 473 PHE 0.025 0.001 PHE C 238 TRP 0.006 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00282 (23982) covalent geometry : angle 0.49861 (32699) SS BOND : bond 0.00209 ( 39) SS BOND : angle 1.51225 ( 78) hydrogen bonds : bond 0.03993 ( 1024) hydrogen bonds : angle 5.23281 ( 2781) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.02529 ( 33) link_NAG-ASN : bond 0.00157 ( 38) link_NAG-ASN : angle 1.42680 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 878 LEU cc_start: 0.9225 (tp) cc_final: 0.8671 (mt) REVERT: B 907 ASN cc_start: 0.8752 (t0) cc_final: 0.8271 (t0) REVERT: C 269 TYR cc_start: 0.7506 (m-80) cc_final: 0.6897 (m-80) REVERT: C 389 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7127 (t0) REVERT: C 421 TYR cc_start: 0.8311 (m-10) cc_final: 0.7335 (m-10) outliers start: 27 outliers final: 21 residues processed: 229 average time/residue: 0.2625 time to fit residues: 97.0824 Evaluate side-chains 220 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 105 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 136 optimal weight: 40.0000 chunk 188 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125244 restraints weight = 90545.811| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.25 r_work: 0.3188 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24070 Z= 0.165 Angle : 0.520 6.949 32924 Z= 0.270 Chirality : 0.044 0.172 3927 Planarity : 0.004 0.044 4159 Dihedral : 5.159 59.632 4206 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.21 % Allowed : 11.53 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2921 helix: 1.56 (0.21), residues: 688 sheet: -0.26 (0.20), residues: 654 loop : -0.98 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.013 0.001 TYR B 369 PHE 0.027 0.001 PHE C 238 TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00380 (23982) covalent geometry : angle 0.50894 (32699) SS BOND : bond 0.00229 ( 39) SS BOND : angle 1.46023 ( 78) hydrogen bonds : bond 0.04136 ( 1024) hydrogen bonds : angle 5.26929 ( 2781) link_BETA1-4 : bond 0.00213 ( 11) link_BETA1-4 : angle 0.99061 ( 33) link_NAG-ASN : bond 0.00186 ( 38) link_NAG-ASN : angle 1.47186 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 878 LEU cc_start: 0.9203 (tp) cc_final: 0.8601 (mt) REVERT: C 269 TYR cc_start: 0.7529 (m-80) cc_final: 0.6884 (m-80) REVERT: C 389 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7159 (t0) REVERT: C 421 TYR cc_start: 0.8361 (m-10) cc_final: 0.7369 (m-10) outliers start: 30 outliers final: 25 residues processed: 228 average time/residue: 0.2296 time to fit residues: 84.4540 Evaluate side-chains 225 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 136 optimal weight: 30.0000 chunk 166 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127877 restraints weight = 90332.484| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.04 r_work: 0.3200 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24070 Z= 0.164 Angle : 0.520 7.152 32924 Z= 0.271 Chirality : 0.044 0.168 3927 Planarity : 0.004 0.043 4159 Dihedral : 5.097 59.989 4206 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.21 % Allowed : 11.77 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.28 (0.15), residues: 2921 helix: 1.56 (0.21), residues: 688 sheet: -0.26 (0.20), residues: 646 loop : -0.94 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.013 0.001 TYR B 369 PHE 0.027 0.001 PHE C 238 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00377 (23982) covalent geometry : angle 0.50819 (32699) SS BOND : bond 0.00228 ( 39) SS BOND : angle 1.51818 ( 78) hydrogen bonds : bond 0.04115 ( 1024) hydrogen bonds : angle 5.24489 ( 2781) link_BETA1-4 : bond 0.00209 ( 11) link_BETA1-4 : angle 0.95586 ( 33) link_NAG-ASN : bond 0.00168 ( 38) link_NAG-ASN : angle 1.43505 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 878 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8629 (mt) REVERT: C 269 TYR cc_start: 0.7470 (m-80) cc_final: 0.6863 (m-80) REVERT: C 389 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7116 (t0) REVERT: C 421 TYR cc_start: 0.8337 (m-10) cc_final: 0.7414 (m-10) outliers start: 30 outliers final: 26 residues processed: 227 average time/residue: 0.2055 time to fit residues: 76.1841 Evaluate side-chains 223 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 271 optimal weight: 0.0770 chunk 185 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129115 restraints weight = 90847.198| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.99 r_work: 0.3216 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24070 Z= 0.132 Angle : 0.504 6.016 32924 Z= 0.262 Chirality : 0.043 0.196 3927 Planarity : 0.003 0.044 4159 Dihedral : 4.965 59.852 4206 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.17 % Allowed : 11.98 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2921 helix: 1.66 (0.21), residues: 688 sheet: -0.17 (0.20), residues: 643 loop : -0.85 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.013 0.001 TYR B 369 PHE 0.026 0.001 PHE C 238 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00304 (23982) covalent geometry : angle 0.49481 (32699) SS BOND : bond 0.00184 ( 39) SS BOND : angle 1.29579 ( 78) hydrogen bonds : bond 0.03939 ( 1024) hydrogen bonds : angle 5.16071 ( 2781) link_BETA1-4 : bond 0.00239 ( 11) link_BETA1-4 : angle 0.96855 ( 33) link_NAG-ASN : bond 0.00145 ( 38) link_NAG-ASN : angle 1.34211 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 878 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8928 (mm) REVERT: B 878 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 907 ASN cc_start: 0.8626 (t0) cc_final: 0.8132 (t0) REVERT: C 269 TYR cc_start: 0.7236 (m-80) cc_final: 0.6702 (m-80) REVERT: C 389 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6881 (t0) REVERT: C 421 TYR cc_start: 0.8201 (m-10) cc_final: 0.7470 (m-10) outliers start: 29 outliers final: 22 residues processed: 226 average time/residue: 0.1951 time to fit residues: 71.5486 Evaluate side-chains 224 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 56 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 275 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128493 restraints weight = 90400.037| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24070 Z= 0.122 Angle : 0.499 6.230 32924 Z= 0.259 Chirality : 0.043 0.169 3927 Planarity : 0.003 0.046 4159 Dihedral : 4.831 59.691 4206 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.01 % Allowed : 12.30 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.07 (0.16), residues: 2921 helix: 1.73 (0.21), residues: 689 sheet: -0.14 (0.20), residues: 644 loop : -0.79 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.013 0.001 TYR B 269 PHE 0.026 0.001 PHE C 238 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00279 (23982) covalent geometry : angle 0.48960 (32699) SS BOND : bond 0.00186 ( 39) SS BOND : angle 1.22007 ( 78) hydrogen bonds : bond 0.03845 ( 1024) hydrogen bonds : angle 5.09531 ( 2781) link_BETA1-4 : bond 0.00236 ( 11) link_BETA1-4 : angle 0.96609 ( 33) link_NAG-ASN : bond 0.00143 ( 38) link_NAG-ASN : angle 1.31322 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9200.76 seconds wall clock time: 156 minutes 34.19 seconds (9394.19 seconds total)