Starting phenix.real_space_refine on Sat Jul 4 22:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyo_23597/07_2026/7lyo_23597.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 15098 2.51 5 N 3886 2.21 5 O 4561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7707 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7705 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.11, per 1000 atoms: 0.22 Number of scatterers: 23649 At special positions: 0 Unit cell: (125.073, 134.694, 194.558, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4561 8.00 N 3886 7.00 C 15098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.04 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=2.01 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 801 " " NAG A1313 " - " ASN A1074 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1098 " " NAG C1313 " - " ASN C1134 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5574 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 46 sheets defined 27.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.522A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.711A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.182A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.871A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.633A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.901A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.547A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.708A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.176A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.037A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.102A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.411A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.898A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.588A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.606A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 removed outlier: 3.667A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.708A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.347A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.848A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.593A 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 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.814A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.844A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.816A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.568A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.920A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.519A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.542A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.321A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.737A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.793A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.679A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.377A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.172A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.557A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.557A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.778A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.352A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.352A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.362A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.486A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.629A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.939A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.334A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.965A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.638A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.638A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.243A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.650A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.608A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.771A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.142A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.512A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) 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: 6.790A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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: 6.715A 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: 3.708A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.514A 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: 6.008A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.500A 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: 4.874A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5932 1.33 - 1.45: 4747 1.45 - 1.58: 13355 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 24162 Sorted by residual: bond pdb=" C5 NAG C1313 " pdb=" O5 NAG C1313 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 24741 2.01 - 4.02: 7439 4.02 - 6.02: 651 6.02 - 8.03: 45 8.03 - 10.04: 6 Bond angle restraints: 32882 Sorted by residual: angle pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " ideal model delta sigma weight residual 112.60 119.58 -6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.47 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CB ASN B 801 " pdb=" CG ASN B 801 " pdb=" ND2 ASN B 801 " ideal model delta sigma weight residual 116.40 124.73 -8.33 1.50e+00 4.44e-01 3.08e+01 ... (remaining 32877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13118 17.90 - 35.80: 727 35.80 - 53.70: 122 53.70 - 71.60: 40 71.60 - 89.50: 19 Dihedral angle restraints: 14026 sinusoidal: 5365 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -177.98 -89.02 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA THR B 581 " pdb=" C THR B 581 " pdb=" N LEU B 582 " pdb=" CA LEU B 582 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 14023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2773 0.101 - 0.202: 1012 0.202 - 0.304: 97 0.304 - 0.405: 12 0.405 - 0.506: 1 Chirality restraints: 3895 Sorted by residual: chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA TYR B 200 " pdb=" N TYR B 200 " pdb=" C TYR B 200 " pdb=" CB TYR B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3892 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.283 2.00e-02 2.50e+03 1.50e-01 5.63e+02 pdb=" CG TRP C 886 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.137 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.216 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.169 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.132 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.137 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN A 331 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.172 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11463 2.99 - 3.47: 22482 3.47 - 3.94: 38969 3.94 - 4.42: 43289 4.42 - 4.90: 73983 Nonbonded interactions: 190186 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.511 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.517 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.528 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.533 3.040 ... (remaining 190181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name \ CA or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 through 1312)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 567 or (resid 568 and (name N or name CA or na \ me C or name O or name CB )) or resid 569 through 582 or (resid 583 and (name N \ or name CA or name C or name O or name CB )) or resid 584 through 585 or (resid \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name \ CA or name C or name O or name CB )) or resid 746 through 747 or (resid 748 and \ (name N or name CA or name C or name O or name CB )) or resid 749 through 810 o \ r (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 13 or (resid 814 and (name N or name CA or name C or name O or name CB )) or res \ id 815 through 827 or resid 855 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 1091 or (res \ id 1092 and (name N or name CA or name C or name O or name CB )) or resid 1093 t \ hrough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147 through 1312)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or na \ me O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (n \ ame N or name CA or name C or name O or name CB )) or resid 310 through 527 or ( \ resid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 \ through 567 or (resid 568 and (name N or name CA or name C or name O or name CB \ )) or resid 569 through 582 or (resid 583 and (name N or name CA or name C or na \ me O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and (n \ ame N or name CA or name C or name O or name CB )) or resid 620 through 813 or ( \ resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name C \ B )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1312)) } 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: 0.010 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.020 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.076 24241 Z= 0.761 Angle : 1.769 10.041 33080 Z= 1.177 Chirality : 0.095 0.506 3895 Planarity : 0.013 0.165 4184 Dihedral : 12.566 89.504 8335 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.43 % Favored : 94.30 % Rotamer: Outliers : 0.43 % Allowed : 2.31 % Favored : 97.25 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 2928 helix: -1.05 (0.17), residues: 703 sheet: 0.58 (0.21), residues: 523 loop : -0.72 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 905 TYR 0.126 0.019 TYR B 421 PHE 0.086 0.012 PHE C 718 TRP 0.283 0.029 TRP C 886 HIS 0.009 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01324 / 0.76 (24162) covalent geometry : angle 1.75020 / 1.18 (32882) SS BOND : bond 0.01263 / 0.76 ( 39) SS BOND : angle 2.18636 / 1.50 ( 78) hydrogen bonds : bond 0.16041 / 10.52 ( 1024) hydrogen bonds : angle 8.40940 / 5.86 ( 2829) link_NAG-ASN : bond 0.01297 / 0.80 ( 40) link_NAG-ASN : angle 4.52555 / 3.11 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 392 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 SER cc_start: 0.7601 (t) cc_final: 0.7068 (t) REVERT: A 394 ASN cc_start: 0.7480 (m-40) cc_final: 0.7252 (m-40) REVERT: A 902 MET cc_start: 0.8632 (mmm) cc_final: 0.8383 (mmm) REVERT: A 950 ASP cc_start: 0.7531 (t70) cc_final: 0.7227 (t0) REVERT: B 54 LEU cc_start: 0.8457 (mt) cc_final: 0.8248 (mp) REVERT: B 347 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.3408 (m-80) REVERT: B 392 PHE cc_start: 0.7502 (m-80) cc_final: 0.7100 (m-10) REVERT: B 572 THR cc_start: 0.8849 (m) cc_final: 0.8334 (m) REVERT: B 584 ILE cc_start: 0.8611 (mm) cc_final: 0.8398 (mt) REVERT: C 428 ASP cc_start: 0.7342 (p0) cc_final: 0.6675 (t70) REVERT: C 469 SER cc_start: 0.7906 (t) cc_final: 0.7609 (m) REVERT: C 902 MET cc_start: 0.8860 (mmm) cc_final: 0.8515 (tpt) REVERT: C 904 TYR cc_start: 0.7874 (m-10) cc_final: 0.7459 (m-10) REVERT: C 979 ASP cc_start: 0.7368 (t0) cc_final: 0.7163 (t0) outliers start: 11 outliers final: 4 residues processed: 401 average time/residue: 0.1799 time to fit residues: 111.7467 Evaluate side-chains 193 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 188 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 347 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 61 ASN B 87 ASN B 394 ASN B 762 GLN B1088 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1002 GLN C1088 HIS C1113 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114030 restraints weight = 33589.107| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.57 r_work: 0.2948 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24241 Z= 0.144 Angle : 0.664 12.483 33080 Z= 0.343 Chirality : 0.047 0.228 3895 Planarity : 0.004 0.036 4184 Dihedral : 5.990 57.290 3192 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.46 % Favored : 97.37 % Rotamer: Outliers : 1.37 % Allowed : 6.90 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 2928 helix: 1.13 (0.20), residues: 681 sheet: 0.38 (0.19), residues: 686 loop : -0.48 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.026 0.002 TYR B 369 PHE 0.021 0.002 PHE A 140 TRP 0.017 0.002 TRP B 64 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (24162) covalent geometry : angle 0.63292 / 0.34 (32882) SS BOND : bond 0.01455 / 0.72 ( 39) SS BOND : angle 1.58458 / 1.06 ( 78) hydrogen bonds : bond 0.04582 / 3.02 ( 1024) hydrogen bonds : angle 6.32808 / 4.40 ( 2829) link_NAG-ASN : bond 0.00303 / 0.20 ( 40) link_NAG-ASN : angle 3.18101 / 2.27 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9490 (t) cc_final: 0.9070 (p) REVERT: A 394 ASN cc_start: 0.8086 (m-40) cc_final: 0.7709 (m-40) REVERT: A 428 ASP cc_start: 0.8766 (p0) cc_final: 0.8453 (p0) REVERT: A 470 THR cc_start: 0.8943 (p) cc_final: 0.8525 (t) REVERT: A 776 LYS cc_start: 0.9000 (tttt) cc_final: 0.8689 (tttm) REVERT: A 950 ASP cc_start: 0.8259 (t70) cc_final: 0.8039 (t0) REVERT: A 957 GLN cc_start: 0.8725 (tp40) cc_final: 0.8485 (tp40) REVERT: B 95 THR cc_start: 0.7783 (p) cc_final: 0.7434 (t) REVERT: B 135 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 347 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.4071 (m-80) REVERT: B 392 PHE cc_start: 0.7629 (m-80) cc_final: 0.7086 (m-10) REVERT: B 515 PHE cc_start: 0.7937 (m-10) cc_final: 0.7614 (m-10) REVERT: B 583 GLU cc_start: 0.8411 (pt0) cc_final: 0.8047 (pm20) REVERT: B 950 ASP cc_start: 0.8782 (t0) cc_final: 0.8497 (t0) REVERT: C 461 LEU cc_start: 0.8955 (mm) cc_final: 0.8750 (mm) REVERT: C 465 GLU cc_start: 0.7844 (tt0) cc_final: 0.7273 (mt-10) REVERT: C 904 TYR cc_start: 0.8130 (m-10) cc_final: 0.7481 (m-10) outliers start: 35 outliers final: 21 residues processed: 243 average time/residue: 0.1426 time to fit residues: 56.5181 Evaluate side-chains 180 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 78 optimal weight: 0.9990 chunk 156 optimal weight: 0.0970 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1119 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114803 restraints weight = 33674.928| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.23 r_work: 0.2952 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 24241 Z= 0.137 Angle : 0.604 12.678 33080 Z= 0.309 Chirality : 0.045 0.221 3895 Planarity : 0.003 0.033 4184 Dihedral : 5.236 56.764 3189 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.33 % Allowed : 8.75 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 2928 helix: 1.42 (0.20), residues: 690 sheet: 0.39 (0.19), residues: 679 loop : -0.37 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 408 TYR 0.022 0.001 TYR C 369 PHE 0.020 0.002 PHE B 201 TRP 0.015 0.001 TRP B 64 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24162) covalent geometry : angle 0.57238 / 0.30 (32882) SS BOND : bond 0.00397 / 0.20 ( 39) SS BOND : angle 2.15324 / 1.36 ( 78) hydrogen bonds : bond 0.04165 / 2.73 ( 1024) hydrogen bonds : angle 5.95871 / 4.17 ( 2829) link_NAG-ASN : bond 0.00274 / 0.18 ( 40) link_NAG-ASN : angle 2.81201 / 2.01 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9476 (t) cc_final: 0.9098 (p) REVERT: A 428 ASP cc_start: 0.8782 (p0) cc_final: 0.8424 (p0) REVERT: A 470 THR cc_start: 0.9004 (p) cc_final: 0.8631 (t) REVERT: A 536 ASN cc_start: 0.8756 (m-40) cc_final: 0.8441 (m110) REVERT: A 776 LYS cc_start: 0.9016 (tttt) cc_final: 0.8627 (tttm) REVERT: B 95 THR cc_start: 0.7750 (p) cc_final: 0.7488 (t) REVERT: B 135 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5995 (t80) REVERT: B 347 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.3994 (m-80) REVERT: B 392 PHE cc_start: 0.7573 (m-80) cc_final: 0.7038 (m-10) REVERT: B 515 PHE cc_start: 0.7832 (m-10) cc_final: 0.7604 (m-10) REVERT: C 239 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: C 357 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7706 (ttt90) REVERT: C 465 GLU cc_start: 0.7827 (tt0) cc_final: 0.7208 (mt-10) REVERT: C 469 SER cc_start: 0.8027 (t) cc_final: 0.7630 (m) outliers start: 34 outliers final: 17 residues processed: 202 average time/residue: 0.1561 time to fit residues: 51.4671 Evaluate side-chains 174 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 34 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 296 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 675 GLN B 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106070 restraints weight = 33608.283| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.77 r_work: 0.3070 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24241 Z= 0.167 Angle : 0.602 15.248 33080 Z= 0.303 Chirality : 0.046 0.622 3895 Planarity : 0.003 0.036 4184 Dihedral : 4.992 57.095 3185 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 1.61 % Allowed : 9.65 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2928 helix: 1.42 (0.20), residues: 690 sheet: 0.31 (0.19), residues: 702 loop : -0.37 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.002 PHE C 823 TRP 0.016 0.001 TRP B 353 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (24162) covalent geometry : angle 0.56871 / 0.30 (32882) SS BOND : bond 0.00342 / 0.20 ( 39) SS BOND : angle 1.96901 / 1.28 ( 78) hydrogen bonds : bond 0.04100 / 2.69 ( 1024) hydrogen bonds : angle 5.85556 / 4.12 ( 2829) link_NAG-ASN : bond 0.00266 / 0.18 ( 40) link_NAG-ASN : angle 2.95077 / 2.13 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9472 (t) cc_final: 0.9107 (p) REVERT: A 394 ASN cc_start: 0.8054 (m-40) cc_final: 0.7709 (m-40) REVERT: A 428 ASP cc_start: 0.8757 (p0) cc_final: 0.8421 (p0) REVERT: A 470 THR cc_start: 0.8991 (p) cc_final: 0.8652 (t) REVERT: A 536 ASN cc_start: 0.8764 (m-40) cc_final: 0.8476 (m110) REVERT: A 776 LYS cc_start: 0.8961 (tttt) cc_final: 0.8590 (tttm) REVERT: B 135 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 269 TYR cc_start: 0.7261 (m-10) cc_final: 0.6944 (m-80) REVERT: B 319 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (mtp85) REVERT: B 347 PHE cc_start: 0.5526 (OUTLIER) cc_final: 0.4009 (m-80) REVERT: B 392 PHE cc_start: 0.7657 (m-80) cc_final: 0.7244 (m-10) REVERT: B 515 PHE cc_start: 0.7960 (m-80) cc_final: 0.7593 (m-10) REVERT: C 129 LYS cc_start: 0.7608 (tttt) cc_final: 0.7199 (ttmt) REVERT: C 197 ILE cc_start: 0.8486 (mm) cc_final: 0.8259 (mm) REVERT: C 239 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: C 357 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7697 (ttt90) REVERT: C 469 SER cc_start: 0.8016 (t) cc_final: 0.7712 (m) outliers start: 41 outliers final: 21 residues processed: 191 average time/residue: 0.1522 time to fit residues: 48.0979 Evaluate side-chains 164 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 166 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107763 restraints weight = 33590.147| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.73 r_work: 0.3056 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24241 Z= 0.198 Angle : 0.606 13.886 33080 Z= 0.306 Chirality : 0.046 0.276 3895 Planarity : 0.004 0.040 4184 Dihedral : 4.869 56.509 3185 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 10.31 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2928 helix: 1.40 (0.20), residues: 690 sheet: 0.34 (0.19), residues: 703 loop : -0.44 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.002 PHE A 140 TRP 0.019 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (24162) covalent geometry : angle 0.57398 / 0.30 (32882) SS BOND : bond 0.00404 / 0.24 ( 39) SS BOND : angle 2.09482 / 1.33 ( 78) hydrogen bonds : bond 0.04194 / 2.75 ( 1024) hydrogen bonds : angle 5.80649 / 4.08 ( 2829) link_NAG-ASN : bond 0.00356 / 0.25 ( 40) link_NAG-ASN : angle 2.84769 / 2.06 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9507 (t) cc_final: 0.9160 (p) REVERT: A 319 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7406 (mtp-110) REVERT: A 414 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8043 (mm-40) REVERT: A 428 ASP cc_start: 0.8732 (p0) cc_final: 0.8412 (p0) REVERT: A 470 THR cc_start: 0.8959 (p) cc_final: 0.8668 (t) REVERT: A 536 ASN cc_start: 0.8784 (m-40) cc_final: 0.8539 (m110) REVERT: A 776 LYS cc_start: 0.8954 (tttt) cc_final: 0.8620 (tttm) REVERT: A 869 MET cc_start: 0.9174 (mtm) cc_final: 0.8919 (mtt) REVERT: B 135 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.6053 (t80) REVERT: B 269 TYR cc_start: 0.7227 (m-10) cc_final: 0.6890 (m-80) REVERT: B 347 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.4015 (m-80) REVERT: B 392 PHE cc_start: 0.7711 (m-80) cc_final: 0.7282 (m-80) REVERT: B 515 PHE cc_start: 0.7923 (m-80) cc_final: 0.7599 (m-10) REVERT: C 239 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: C 240 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8385 (t) REVERT: C 357 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7768 (ttt90) REVERT: C 465 GLU cc_start: 0.7596 (tt0) cc_final: 0.7036 (mt-10) REVERT: C 469 SER cc_start: 0.8132 (t) cc_final: 0.7837 (m) REVERT: C 855 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6002 (m-80) outliers start: 49 outliers final: 31 residues processed: 191 average time/residue: 0.1383 time to fit residues: 44.0814 Evaluate side-chains 174 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 141 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 218 GLN C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108488 restraints weight = 33730.728| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.79 r_work: 0.3039 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24241 Z= 0.151 Angle : 0.565 14.918 33080 Z= 0.285 Chirality : 0.045 0.447 3895 Planarity : 0.003 0.035 4184 Dihedral : 4.683 55.834 3185 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 2.00 % Allowed : 10.98 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2928 helix: 1.64 (0.20), residues: 677 sheet: 0.31 (0.19), residues: 676 loop : -0.46 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE A 140 TRP 0.019 0.001 TRP B 353 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (24162) covalent geometry : angle 0.53420 / 0.28 (32882) SS BOND : bond 0.00362 / 0.22 ( 39) SS BOND : angle 1.87946 / 1.22 ( 78) hydrogen bonds : bond 0.03835 / 2.50 ( 1024) hydrogen bonds : angle 5.66499 / 3.99 ( 2829) link_NAG-ASN : bond 0.00325 / 0.24 ( 40) link_NAG-ASN : angle 2.73851 / 2.00 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9470 (t) cc_final: 0.9128 (p) REVERT: A 319 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7471 (mtp-110) REVERT: A 414 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8073 (mm-40) REVERT: A 428 ASP cc_start: 0.8747 (p0) cc_final: 0.8440 (p0) REVERT: A 470 THR cc_start: 0.8934 (p) cc_final: 0.8625 (t) REVERT: A 536 ASN cc_start: 0.8783 (m-40) cc_final: 0.8535 (m110) REVERT: A 776 LYS cc_start: 0.8932 (tttt) cc_final: 0.8675 (tttm) REVERT: A 869 MET cc_start: 0.9172 (mtm) cc_final: 0.8911 (mtt) REVERT: B 135 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 269 TYR cc_start: 0.7155 (m-10) cc_final: 0.6848 (m-80) REVERT: B 319 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8238 (mtp85) REVERT: B 347 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.3822 (m-80) REVERT: B 392 PHE cc_start: 0.7872 (m-80) cc_final: 0.7469 (m-80) REVERT: B 515 PHE cc_start: 0.7892 (m-80) cc_final: 0.7611 (m-10) REVERT: C 129 LYS cc_start: 0.7730 (tttt) cc_final: 0.7456 (tttm) REVERT: C 239 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8599 (tm-30) REVERT: C 240 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8369 (t) REVERT: C 357 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (ttt90) REVERT: C 465 GLU cc_start: 0.7630 (tt0) cc_final: 0.7046 (mt-10) REVERT: C 469 SER cc_start: 0.8136 (t) cc_final: 0.7849 (m) REVERT: C 855 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6002 (m-80) outliers start: 51 outliers final: 33 residues processed: 196 average time/residue: 0.1531 time to fit residues: 49.6120 Evaluate side-chains 176 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 258 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 173 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1083 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106981 restraints weight = 33571.196| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.79 r_work: 0.3065 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24241 Z= 0.115 Angle : 0.536 13.923 33080 Z= 0.271 Chirality : 0.044 0.353 3895 Planarity : 0.003 0.034 4184 Dihedral : 4.486 55.286 3185 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 11.57 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2928 helix: 1.84 (0.21), residues: 678 sheet: 0.39 (0.19), residues: 671 loop : -0.38 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.018 0.001 TYR C 369 PHE 0.020 0.001 PHE B 201 TRP 0.018 0.001 TRP B 353 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (24162) covalent geometry : angle 0.50989 / 0.26 (32882) SS BOND : bond 0.00353 / 0.21 ( 39) SS BOND : angle 1.58072 / 1.05 ( 78) hydrogen bonds : bond 0.03524 / 2.30 ( 1024) hydrogen bonds : angle 5.50272 / 3.88 ( 2829) link_NAG-ASN : bond 0.00302 / 0.22 ( 40) link_NAG-ASN : angle 2.53875 / 1.86 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9370 (t) cc_final: 0.9024 (p) REVERT: A 319 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7492 (mtp-110) REVERT: A 414 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8131 (mm-40) REVERT: A 428 ASP cc_start: 0.8710 (p0) cc_final: 0.8446 (p0) REVERT: A 470 THR cc_start: 0.8908 (p) cc_final: 0.8605 (t) REVERT: A 536 ASN cc_start: 0.8716 (m-40) cc_final: 0.8476 (m110) REVERT: A 592 PHE cc_start: 0.8588 (p90) cc_final: 0.8302 (p90) REVERT: A 776 LYS cc_start: 0.8903 (tttt) cc_final: 0.8673 (tttm) REVERT: A 869 MET cc_start: 0.9126 (mtm) cc_final: 0.8817 (mtt) REVERT: B 135 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.6058 (t80) REVERT: B 269 TYR cc_start: 0.7063 (m-10) cc_final: 0.6682 (m-80) REVERT: B 347 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.3882 (m-80) REVERT: B 392 PHE cc_start: 0.7869 (m-80) cc_final: 0.7508 (m-80) REVERT: B 515 PHE cc_start: 0.7894 (m-80) cc_final: 0.7633 (m-10) REVERT: C 239 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8592 (tm-30) REVERT: C 357 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7852 (ttt90) REVERT: C 465 GLU cc_start: 0.7574 (tt0) cc_final: 0.7083 (mt-10) REVERT: C 469 SER cc_start: 0.8103 (t) cc_final: 0.7834 (m) REVERT: C 855 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: C 983 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7769 (ttp-110) outliers start: 44 outliers final: 31 residues processed: 191 average time/residue: 0.1544 time to fit residues: 48.9170 Evaluate side-chains 177 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 66 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 0.0060 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108528 restraints weight = 33930.637| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.68 r_work: 0.3007 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24241 Z= 0.256 Angle : 0.635 13.908 33080 Z= 0.321 Chirality : 0.047 0.331 3895 Planarity : 0.004 0.036 4184 Dihedral : 4.778 54.567 3185 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.04 % Allowed : 11.76 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 2928 helix: 1.38 (0.20), residues: 685 sheet: 0.19 (0.19), residues: 702 loop : -0.49 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.021 0.002 TYR B1067 PHE 0.023 0.002 PHE A 140 TRP 0.018 0.001 TRP B 353 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 (24162) covalent geometry : angle 0.60882 / 0.31 (32882) SS BOND : bond 0.00474 / 0.30 ( 39) SS BOND : angle 1.89740 / 1.23 ( 78) hydrogen bonds : bond 0.04421 / 2.91 ( 1024) hydrogen bonds : angle 5.78000 / 4.06 ( 2829) link_NAG-ASN : bond 0.00346 / 0.24 ( 40) link_NAG-ASN : angle 2.71700 / 1.97 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9455 (t) cc_final: 0.9107 (p) REVERT: A 319 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7643 (mtp-110) REVERT: A 414 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8135 (mm-40) REVERT: A 428 ASP cc_start: 0.8704 (p0) cc_final: 0.8386 (p0) REVERT: A 470 THR cc_start: 0.8968 (p) cc_final: 0.8646 (t) REVERT: A 498 GLN cc_start: 0.8071 (mp10) cc_final: 0.7494 (mp10) REVERT: A 776 LYS cc_start: 0.8972 (tttt) cc_final: 0.8671 (tttm) REVERT: A 869 MET cc_start: 0.9113 (mtm) cc_final: 0.8844 (mtt) REVERT: B 347 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.4040 (m-80) REVERT: B 515 PHE cc_start: 0.7895 (m-80) cc_final: 0.7579 (m-80) REVERT: C 129 LYS cc_start: 0.7827 (tttt) cc_final: 0.7235 (tttt) REVERT: C 239 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8577 (tm-30) REVERT: C 357 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7888 (ttt90) REVERT: C 452 LEU cc_start: 0.8761 (mp) cc_final: 0.8445 (mt) REVERT: C 465 GLU cc_start: 0.7521 (tt0) cc_final: 0.6972 (mt-10) REVERT: C 469 SER cc_start: 0.8079 (t) cc_final: 0.7799 (m) REVERT: C 855 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: C 904 TYR cc_start: 0.8070 (m-10) cc_final: 0.7670 (m-10) outliers start: 52 outliers final: 40 residues processed: 181 average time/residue: 0.1437 time to fit residues: 43.4808 Evaluate side-chains 179 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 150 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112342 restraints weight = 33584.860| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.76 r_work: 0.3048 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24241 Z= 0.127 Angle : 0.552 13.403 33080 Z= 0.276 Chirality : 0.044 0.329 3895 Planarity : 0.003 0.039 4184 Dihedral : 4.480 54.164 3185 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 1.73 % Allowed : 12.12 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2928 helix: 1.70 (0.20), residues: 686 sheet: 0.33 (0.19), residues: 683 loop : -0.41 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.018 0.001 TYR C 489 PHE 0.030 0.001 PHE B 392 TRP 0.020 0.001 TRP B 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24162) covalent geometry : angle 0.52699 / 0.27 (32882) SS BOND : bond 0.00369 / 0.23 ( 39) SS BOND : angle 1.56875 / 1.04 ( 78) hydrogen bonds : bond 0.03591 / 2.34 ( 1024) hydrogen bonds : angle 5.49187 / 3.86 ( 2829) link_NAG-ASN : bond 0.00309 / 0.22 ( 40) link_NAG-ASN : angle 2.48903 / 1.82 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9398 (t) cc_final: 0.9043 (p) REVERT: A 319 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7635 (mtp-110) REVERT: A 414 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8149 (mm-40) REVERT: A 428 ASP cc_start: 0.8686 (p0) cc_final: 0.8404 (p0) REVERT: A 470 THR cc_start: 0.9010 (p) cc_final: 0.8703 (t) REVERT: A 776 LYS cc_start: 0.8962 (tttt) cc_final: 0.8691 (tttm) REVERT: A 1128 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8660 (m) REVERT: B 347 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.3938 (m-80) REVERT: B 351 TYR cc_start: 0.7716 (p90) cc_final: 0.7428 (p90) REVERT: C 239 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: C 357 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7869 (ttt90) REVERT: C 452 LEU cc_start: 0.8822 (mp) cc_final: 0.8479 (mt) REVERT: C 465 GLU cc_start: 0.7499 (tt0) cc_final: 0.7044 (mt-10) REVERT: C 855 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.5960 (m-80) outliers start: 44 outliers final: 36 residues processed: 186 average time/residue: 0.1370 time to fit residues: 42.7598 Evaluate side-chains 183 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 245 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 208 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111512 restraints weight = 33686.570| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.73 r_work: 0.3044 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24241 Z= 0.141 Angle : 0.560 13.296 33080 Z= 0.279 Chirality : 0.044 0.318 3895 Planarity : 0.003 0.039 4184 Dihedral : 4.440 53.645 3185 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.65 % Allowed : 12.47 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2928 helix: 1.74 (0.20), residues: 685 sheet: 0.33 (0.19), residues: 685 loop : -0.41 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE B 392 TRP 0.020 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (24162) covalent geometry : angle 0.53601 / 0.27 (32882) SS BOND : bond 0.00373 / 0.23 ( 39) SS BOND : angle 1.57589 / 1.04 ( 78) hydrogen bonds : bond 0.03670 / 2.40 ( 1024) hydrogen bonds : angle 5.45360 / 3.83 ( 2829) link_NAG-ASN : bond 0.00309 / 0.22 ( 40) link_NAG-ASN : angle 2.44624 / 1.79 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9397 (t) cc_final: 0.9058 (p) REVERT: A 319 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7749 (mtp-110) REVERT: A 414 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 428 ASP cc_start: 0.8711 (p0) cc_final: 0.8445 (p0) REVERT: A 776 LYS cc_start: 0.8931 (tttt) cc_final: 0.8683 (tttm) REVERT: A 1128 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8632 (m) REVERT: B 347 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.3934 (m-80) REVERT: B 351 TYR cc_start: 0.7680 (p90) cc_final: 0.7390 (p90) REVERT: C 239 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: C 357 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (ttt90) REVERT: C 452 LEU cc_start: 0.8826 (mp) cc_final: 0.8485 (mt) REVERT: C 465 GLU cc_start: 0.7460 (tt0) cc_final: 0.7004 (mt-10) REVERT: C 855 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: C 983 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7834 (mtp180) outliers start: 42 outliers final: 35 residues processed: 179 average time/residue: 0.1441 time to fit residues: 43.5469 Evaluate side-chains 178 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 205 optimal weight: 10.0000 chunk 272 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 292 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113448 restraints weight = 33587.087| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.69 r_work: 0.3088 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24241 Z= 0.111 Angle : 0.553 16.636 33080 Z= 0.273 Chirality : 0.044 0.317 3895 Planarity : 0.003 0.039 4184 Dihedral : 4.294 53.566 3185 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.65 % Allowed : 12.51 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2928 helix: 1.90 (0.20), residues: 685 sheet: 0.41 (0.19), residues: 667 loop : -0.33 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.021 0.001 TYR C 489 PHE 0.022 0.001 PHE A 140 TRP 0.022 0.001 TRP B 353 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24162) covalent geometry : angle 0.53197 / 0.27 (32882) SS BOND : bond 0.00338 / 0.20 ( 39) SS BOND : angle 1.43886 / 0.97 ( 78) hydrogen bonds : bond 0.03405 / 2.22 ( 1024) hydrogen bonds : angle 5.31771 / 3.74 ( 2829) link_NAG-ASN : bond 0.00313 / 0.23 ( 40) link_NAG-ASN : angle 2.32889 / 1.72 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5804.42 seconds wall clock time: 100 minutes 14.43 seconds (6014.43 seconds total)